Diff for /imach/src/imach.c between versions 1.2 and 1.121

version 1.2, 2001/03/13 18:10:26 version 1.121, 2006/03/16 17:45:01
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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 1.121  2006/03/16 17:45:01  lievre
   individuals from different ages are interviewed on their health status    * imach.c (Module): Comments concerning covariates added
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    * imach.c (Module): refinements in the computation of lli if
   Health expectancies are computed from the transistions observed between    status=-2 in order to have more reliable computation if stepm is
   waves and are computed for each degree of severity of disability (number    not 1 month. Version 0.98f
   of life states). More degrees you consider, more time is necessary to  
   reach the Maximum Likelihood of the parameters involved in the model.    Revision 1.120  2006/03/16 15:10:38  lievre
   The simplest model is the multinomial logistic model where pij is    (Module): refinements in the computation of lli if
   the probabibility to be observed in state j at the second wave conditional    status=-2 in order to have more reliable computation if stepm is
   to be observed in state i at the first wave. Therefore the model is:    not 1 month. Version 0.98f
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'  
   is a covariate. If you want to have a more complex model than "constant and    Revision 1.119  2006/03/15 17:42:26  brouard
   age", you should modify the program where the markup    (Module): Bug if status = -2, the loglikelihood was
     *Covariates have to be included here again* invites you to do it.    computed as likelihood omitting the logarithm. Version O.98e
   More covariates you add, less is the speed of the convergence.  
     Revision 1.118  2006/03/14 18:20:07  brouard
   The advantage that this computer programme claims, comes from that if the    (Module): varevsij Comments added explaining the second
   delay between waves is not identical for each individual, or if some    table of variances if popbased=1 .
   individual missed an interview, the information is not rounded or lost, but    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   taken into account using an interpolation or extrapolation.    (Module): Function pstamp added
   hPijx is the probability to be    (Module): Version 0.98d
   observed in state i at age x+h conditional to the observed state i at age  
   x. The delay 'h' can be split into an exact number (nh*stepm) of    Revision 1.117  2006/03/14 17:16:22  brouard
   unobserved intermediate  states. This elementary transition (by month or    (Module): varevsij Comments added explaining the second
   quarter trimester, semester or year) is model as a multinomial logistic.    table of variances if popbased=1 .
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   and the contribution of each individual to the likelihood is simply hPijx.    (Module): Function pstamp added
     (Module): Version 0.98d
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.116  2006/03/06 10:29:27  brouard
      (Module): Variance-covariance wrong links and
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    varian-covariance of ej. is needed (Saito).
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.115  2006/02/27 12:17:45  brouard
   from the European Union.    (Module): One freematrix added in mlikeli! 0.98c
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.114  2006/02/26 12:57:58  brouard
   can be accessed at http://euroreves.ined.fr/imach .    (Module): Some improvements in processing parameter
   **********************************************************************/    filename with strsep.
    
 #include <math.h>    Revision 1.113  2006/02/24 14:20:24  brouard
 #include <stdio.h>    (Module): Memory leaks checks with valgrind and:
 #include <stdlib.h>    datafile was not closed, some imatrix were not freed and on matrix
 #include <unistd.h>    allocation too.
   
 #define MAXLINE 256    Revision 1.112  2006/01/30 09:55:26  brouard
 #define FILENAMELENGTH 80    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 /*#define DEBUG*/  
 #define windows    Revision 1.111  2006/01/25 20:38:18  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    (Module): Comments can be added in data file. Missing date values
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    can be a simple dot '.'.
   
 #define NINTERVMAX 8    Revision 1.110  2006/01/25 00:51:50  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    (Module): Lots of cleaning and bugs added (Gompertz)
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.109  2006/01/24 19:37:15  brouard
 #define MAXN 80000    (Module): Comments (lines starting with a #) are allowed in data.
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.108  2006/01/19 18:05:42  lievre
 #define AGEBASE 40    Gnuplot problem appeared...
     To be fixed
   
 int nvar;    Revision 1.107  2006/01/19 16:20:37  brouard
 static int cptcov;    Test existence of gnuplot in imach path
 int cptcovn;  
 int npar=NPARMAX;    Revision 1.106  2006/01/19 13:24:36  brouard
 int nlstate=2; /* Number of live states */    Some cleaning and links added in html output
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.105  2006/01/05 20:23:19  lievre
     *** empty log message ***
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.104  2005/09/30 16:11:43  lievre
 int mle, weightopt;    (Module): sump fixed, loop imx fixed, and simplifications.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Module): If the status is missing at the last wave but we know
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    that the person is alive, then we can code his/her status as -2
 double **oldm, **newm, **savm; /* Working pointers to matrices */    (instead of missing=-1 in earlier versions) and his/her
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    contributions to the likelihood is 1 - Prob of dying from last
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 FILE *ficgp, *fichtm;    the healthy state at last known wave). Version is 0.98
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.103  2005/09/30 15:54:49  lievre
  FILE  *ficresvij;    (Module): sump fixed, loop imx fixed, and simplifications.
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.102  2004/09/15 17:31:30  brouard
   char fileresvpl[FILENAMELENGTH];    Add the possibility to read data file including tab characters.
   
     Revision 1.101  2004/09/15 10:38:38  brouard
     Fix on curr_time
   
 #define NR_END 1    Revision 1.100  2004/07/12 18:29:06  brouard
 #define FREE_ARG char*    Add version for Mac OS X. Just define UNIX in Makefile
 #define FTOL 1.0e-10  
     Revision 1.99  2004/06/05 08:57:40  brouard
 #define NRANSI    *** empty log message ***
 #define ITMAX 200  
     Revision 1.98  2004/05/16 15:05:56  brouard
 #define TOL 2.0e-4    New version 0.97 . First attempt to estimate force of mortality
     directly from the data i.e. without the need of knowing the health
 #define CGOLD 0.3819660    state at each age, but using a Gompertz model: log u =a + b*age .
 #define ZEPS 1.0e-10    This is the basic analysis of mortality and should be done before any
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    other analysis, in order to test if the mortality estimated from the
     cross-longitudinal survey is different from the mortality estimated
 #define GOLD 1.618034    from other sources like vital statistic data.
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    The same imach parameter file can be used but the option for mle should be -3.
   
 static double maxarg1,maxarg2;    Agnès, who wrote this part of the code, tried to keep most of the
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    former routines in order to include the new code within the former code.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      The output is very simple: only an estimate of the intercept and of
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    the slope with 95% confident intervals.
 #define rint(a) floor(a+0.5)  
     Current limitations:
 static double sqrarg;    A) Even if you enter covariates, i.e. with the
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    B) There is no computation of Life Expectancy nor Life Table.
   
 int imx;    Revision 1.97  2004/02/20 13:25:42  lievre
 int stepm;    Version 0.96d. Population forecasting command line is (temporarily)
 /* Stepm, step in month: minimum step interpolation*/    suppressed.
   
 int m,nb;    Revision 1.96  2003/07/15 15:38:55  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    rewritten within the same printf. Workaround: many printfs.
 double **pmmij;  
     Revision 1.95  2003/07/08 07:54:34  brouard
 double *weight;    * imach.c (Repository):
 int **s; /* Status */    (Repository): Using imachwizard code to output a more meaningful covariance
 double *agedc, **covar, idx;    matrix (cov(a12,c31) instead of numbers.
 int **nbcode, *Tcode, *Tvar, **codtab;  
     Revision 1.94  2003/06/27 13:00:02  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Just cleaning
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.93  2003/06/25 16:33:55  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 /******************************************/    exist so I changed back to asctime which exists.
     (Module): Version 0.96b
 void replace(char *s, char*t)  
 {    Revision 1.92  2003/06/25 16:30:45  brouard
   int i;    (Module): On windows (cygwin) function asctime_r doesn't
   int lg=20;    exist so I changed back to asctime which exists.
   i=0;  
   lg=strlen(t);    Revision 1.91  2003/06/25 15:30:29  brouard
   for(i=0; i<= lg; i++) {    * imach.c (Repository): Duplicated warning errors corrected.
     (s[i] = t[i]);    (Repository): Elapsed time after each iteration is now output. It
     if (t[i]== '\\') s[i]='/';    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.
   
 int nbocc(char *s, char occ)    Revision 1.90  2003/06/24 12:34:15  brouard
 {    (Module): Some bugs corrected for windows. Also, when
   int i,j=0;    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(s);    Revision 1.89  2003/06/24 12:30:52  brouard
   for(i=0; i<= lg; i++) {    (Module): Some bugs corrected for windows. Also, when
   if  (s[i] == occ ) j++;    mle=-1 a template is output in file "or"mypar.txt with the design
   }    of the covariance matrix to be input.
   return j;  
 }    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.
 void cutv(char *u,char *v, char*t, char occ)  
 {    Revision 1.87  2003/06/18 12:26:01  brouard
   int i,lg,j,p;    Version 0.96
   i=0;  
   if (t[0]== occ) p=0;    Revision 1.86  2003/06/17 20:04:08  brouard
   for(j=0; j<=strlen(t)-1; j++) {    (Module): Change position of html and gnuplot routines and added
     if((t[j]!= occ) && (t[j+1]==occ)) p=j+1;    routine fileappend.
   }  
     Revision 1.85  2003/06/17 13:12:43  brouard
   lg=strlen(t);    * imach.c (Repository): Check when date of death was earlier that
   for(j=0; j<p; j++) {    current date of interview. It may happen when the death was just
     (u[j] = t[j]);    prior to the death. In this case, dh was negative and likelihood
     u[p]='\0';    was wrong (infinity). We still send an "Error" but patch by
   }    assuming that the date of death was just one stepm after the
     interview.
    for(j=0; j<= lg; j++) {    (Repository): Because some people have very long ID (first column)
     if (j>=(p+1))(v[j-p-1] = t[j]);    we changed int to long in num[] and we added a new lvector for
   }    memory allocation. But we also truncated to 8 characters (left
 }    truncation)
     (Repository): No more line truncation errors.
   
 /********************** nrerror ********************/    Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
 void nrerror(char error_text[])    place. It differs from routine "prevalence" which may be called
 {    many times. Probs is memory consuming and must be used with
   fprintf(stderr,"ERREUR ...\n");    parcimony.
   fprintf(stderr,"%s\n",error_text);    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   exit(1);  
 }    Revision 1.83  2003/06/10 13:39:11  lievre
 /*********************** vector *******************/    *** empty log message ***
 double *vector(int nl, int nh)  
 {    Revision 1.82  2003/06/05 15:57:20  brouard
   double *v;    Add log in  imach.c and  fullversion number is now printed.
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  */
   return v-nl+NR_END;  /*
 }     Interpolated Markov Chain
   
 /************************ free vector ******************/    Short summary of the programme:
 void free_vector(double*v, int nl, int nh)    
 {    This program computes Healthy Life Expectancies from
   free((FREE_ARG)(v+nl-NR_END));    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 }    first survey ("cross") where individuals from different ages are
     interviewed on their health status or degree of disability (in the
 /************************ivector *******************************/    case of a health survey which is our main interest) -2- at least a
 int *ivector(long nl,long nh)    second wave of interviews ("longitudinal") which measure each change
 {    (if any) in individual health status.  Health expectancies are
   int *v;    computed from the time spent in each health state according to a
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    model. More health states you consider, more time is necessary to reach the
   if (!v) nrerror("allocation failure in ivector");    Maximum Likelihood of the parameters involved in the model.  The
   return v-nl+NR_END;    simplest model is the multinomial logistic model where pij is the
 }    probability to be observed in state j at the second wave
     conditional to be observed in state i at the first wave. Therefore
 /******************free ivector **************************/    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 void free_ivector(int *v, long nl, long nh)    'age' is age and 'sex' is a covariate. If you want to have a more
 {    complex model than "constant and age", you should modify the program
   free((FREE_ARG)(v+nl-NR_END));    where the markup *Covariates have to be included here again* invites
 }    you to do it.  More covariates you add, slower the
     convergence.
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)    The advantage of this computer programme, compared to a simple
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    multinomial logistic model, is clear when the delay between waves is not
 {    identical for each individual. Also, if a individual missed an
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    intermediate interview, the information is lost, but taken into
   int **m;    account using an interpolation or extrapolation.  
    
   /* allocate pointers to rows */    hPijx is the probability to be observed in state i at age x+h
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    conditional to the observed state i at age x. The delay 'h' can be
   if (!m) nrerror("allocation failure 1 in matrix()");    split into an exact number (nh*stepm) of unobserved intermediate
   m += NR_END;    states. This elementary transition (by month, quarter,
   m -= nrl;    semester or year) is modelled as a multinomial logistic.  The hPx
      matrix is simply the matrix product of nh*stepm elementary matrices
      and the contribution of each individual to the likelihood is simply
   /* allocate rows and set pointers to them */    hPijx.
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Also this programme outputs the covariance matrix of the parameters but also
   m[nrl] += NR_END;    of the life expectancies. It also computes the period (stable) prevalence. 
   m[nrl] -= ncl;    
      Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;             Institut national d'études démographiques, Paris.
      This software have been partly granted by Euro-REVES, a concerted action
   /* return pointer to array of pointers to rows */    from the European Union.
   return m;    It is copyrighted identically to a GNU software product, ie programme and
 }    software can be distributed freely for non commercial use. Latest version
     can be accessed at http://euroreves.ined.fr/imach .
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
       int **m;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
       long nch,ncl,nrh,nrl;    
      /* free an int matrix allocated by imatrix() */    **********************************************************************/
 {  /*
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    main
   free((FREE_ARG) (m+nrl-NR_END));    read parameterfile
 }    read datafile
     concatwav
 /******************* matrix *******************************/    freqsummary
 double **matrix(long nrl, long nrh, long ncl, long nch)    if (mle >= 1)
 {      mlikeli
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    print results files
   double **m;    if mle==1 
        computes hessian
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    read end of parameter file: agemin, agemax, bage, fage, estepm
   if (!m) nrerror("allocation failure 1 in matrix()");        begin-prev-date,...
   m += NR_END;    open gnuplot file
   m -= nrl;    open html file
     period (stable) prevalence
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));     for age prevalim()
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    h Pij x
   m[nrl] += NR_END;    variance of p varprob
   m[nrl] -= ncl;    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Variance-covariance of DFLE
   return m;    prevalence()
 }     movingaverage()
     varevsij() 
 /*************************free matrix ************************/    if popbased==1 varevsij(,popbased)
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    total life expectancies
 {    Variance of period (stable) prevalence
   free((FREE_ARG)(m[nrl]+ncl-NR_END));   end
   free((FREE_ARG)(m+nrl-NR_END));  */
 }  
   
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)   
 {  #include <math.h>
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  #include <stdio.h>
   double ***m;  #include <stdlib.h>
   #include <string.h>
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #include <unistd.h>
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  #include <limits.h>
   m -= nrl;  #include <sys/types.h>
   #include <sys/stat.h>
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #include <errno.h>
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  extern int errno;
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  /* #include <sys/time.h> */
   #include <time.h>
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #include "timeval.h"
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  /* #include <libintl.h> */
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  /* #define _(String) gettext (String) */
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  #define MAXLINE 256
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;  #define GNUPLOTPROGRAM "gnuplot"
    /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   for (i=nrl+1; i<=nrh; i++) {  #define FILENAMELENGTH 132
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       m[i][j]=m[i][j-1]+nlay;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   }  
   return m;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 }  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 /*************************free ma3x ************************/  #define NINTERVMAX 8
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 {  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define NCOVMAX 8 /* Maximum number of covariates */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define MAXN 20000
   free((FREE_ARG)(m+nrl-NR_END));  #define YEARM 12. /* Number of months per year */
 }  #define AGESUP 130
   #define AGEBASE 40
 /***************** f1dim *************************/  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 extern int ncom;  #ifdef UNIX
 extern double *pcom,*xicom;  #define DIRSEPARATOR '/'
 extern double (*nrfunc)(double []);  #define CHARSEPARATOR "/"
    #define ODIRSEPARATOR '\\'
 double f1dim(double x)  #else
 {  #define DIRSEPARATOR '\\'
   int j;  #define CHARSEPARATOR "\\"
   double f;  #define ODIRSEPARATOR '/'
   double *xt;  #endif
    
   xt=vector(1,ncom);  /* $Id$ */
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  /* $State$ */
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  char version[]="Imach version 0.98f, March 2006, INED-EUROREVES-Institut de longevite ";
   return f;  char fullversion[]="$Revision$ $Date$"; 
 }  char strstart[80];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 /*****************brent *************************/  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int nvar;
 {  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   int iter;  int npar=NPARMAX;
   double a,b,d,etemp;  int nlstate=2; /* Number of live states */
   double fu,fv,fw,fx;  int ndeath=1; /* Number of dead states */
   double ftemp;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  int popbased=0;
   double e=0.0;  
    int *wav; /* Number of waves for this individuual 0 is possible */
   a=(ax < cx ? ax : cx);  int maxwav; /* Maxim number of waves */
   b=(ax > cx ? ax : cx);  int jmin, jmax; /* min, max spacing between 2 waves */
   x=w=v=bx;  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   fw=fv=fx=(*f)(x);  int gipmx, gsw; /* Global variables on the number of contributions 
   for (iter=1;iter<=ITMAX;iter++) {                     to the likelihood and the sum of weights (done by funcone)*/
     xm=0.5*(a+b);  int mle, weightopt;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     printf(".");fflush(stdout);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 #ifdef DEBUG             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     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);  double jmean; /* Mean space between 2 waves */
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  double **oldm, **newm, **savm; /* Working pointers to matrices */
 #endif  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       *xmin=x;  FILE *ficlog, *ficrespow;
       return fx;  int globpr; /* Global variable for printing or not */
     }  double fretone; /* Only one call to likelihood */
     ftemp=fu;  long ipmx; /* Number of contributions */
     if (fabs(e) > tol1) {  double sw; /* Sum of weights */
       r=(x-w)*(fx-fv);  char filerespow[FILENAMELENGTH];
       q=(x-v)*(fx-fw);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       p=(x-v)*q-(x-w)*r;  FILE *ficresilk;
       q=2.0*(q-r);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       if (q > 0.0) p = -p;  FILE *ficresprobmorprev;
       q=fabs(q);  FILE *fichtm, *fichtmcov; /* Html File */
       etemp=e;  FILE *ficreseij;
       e=d;  char filerese[FILENAMELENGTH];
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  FILE *ficresstdeij;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  char fileresstde[FILENAMELENGTH];
       else {  FILE *ficrescveij;
         d=p/q;  char filerescve[FILENAMELENGTH];
         u=x+d;  FILE  *ficresvij;
         if (u-a < tol2 || b-u < tol2)  char fileresv[FILENAMELENGTH];
           d=SIGN(tol1,xm-x);  FILE  *ficresvpl;
       }  char fileresvpl[FILENAMELENGTH];
     } else {  char title[MAXLINE];
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     }  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     fu=(*f)(u);  char command[FILENAMELENGTH];
     if (fu <= fx) {  int  outcmd=0;
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
         SHFT(fv,fw,fx,fu)  
         } else {  char filelog[FILENAMELENGTH]; /* Log file */
           if (u < x) a=u; else b=u;  char filerest[FILENAMELENGTH];
           if (fu <= fw || w == x) {  char fileregp[FILENAMELENGTH];
             v=w;  char popfile[FILENAMELENGTH];
             w=u;  
             fv=fw;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
             v=u;  struct timezone tzp;
             fv=fu;  extern int gettimeofday();
           }  struct tm tmg, tm, tmf, *gmtime(), *localtime();
         }  long time_value;
   }  extern long time();
   nrerror("Too many iterations in brent");  char strcurr[80], strfor[80];
   *xmin=x;  
   return fx;  char *endptr;
 }  long lval;
   
 /****************** mnbrak ***********************/  #define NR_END 1
   #define FREE_ARG char*
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #define FTOL 1.0e-10
             double (*func)(double))  
 {  #define NRANSI 
   double ulim,u,r,q, dum;  #define ITMAX 200 
   double fu;  
    #define TOL 2.0e-4 
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);  #define CGOLD 0.3819660 
   if (*fb > *fa) {  #define ZEPS 1.0e-10 
     SHFT(dum,*ax,*bx,dum)  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       SHFT(dum,*fb,*fa,dum)  
       }  #define GOLD 1.618034 
   *cx=(*bx)+GOLD*(*bx-*ax);  #define GLIMIT 100.0 
   *fc=(*func)(*cx);  #define TINY 1.0e-20 
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  static double maxarg1,maxarg2;
     q=(*bx-*cx)*(*fb-*fa);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     if ((*bx-u)*(u-*cx) > 0.0) {  #define rint(a) floor(a+0.5)
       fu=(*func)(u);  
     } else if ((*cx-u)*(u-ulim) > 0.0) {  static double sqrarg;
       fu=(*func)(u);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       if (fu < *fc) {  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  int agegomp= AGEGOMP;
           SHFT(*fb,*fc,fu,(*func)(u))  
           }  int imx; 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  int stepm=1;
       u=ulim;  /* Stepm, step in month: minimum step interpolation*/
       fu=(*func)(u);  
     } else {  int estepm;
       u=(*cx)+GOLD*(*cx-*bx);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       fu=(*func)(u);  
     }  int m,nb;
     SHFT(*ax,*bx,*cx,u)  long *num;
       SHFT(*fa,*fb,*fc,fu)  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       }  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 }  double **pmmij, ***probs;
   double *ageexmed,*agecens;
 /*************** linmin ************************/  double dateintmean=0;
   
 int ncom;  double *weight;
 double *pcom,*xicom;  int **s; /* Status */
 double (*nrfunc)(double []);  double *agedc, **covar, idx;
    int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  double *lsurv, *lpop, *tpop;
 {  
   double brent(double ax, double bx, double cx,  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
                double (*f)(double), double tol, double *xmin);  double ftolhess; /* Tolerance for computing hessian */
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  /**************** split *************************/
               double *fc, double (*func)(double));  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   int j;  {
   double xx,xmin,bx,ax;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   double fx,fb,fa;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
      */ 
   ncom=n;    char  *ss;                            /* pointer */
   pcom=vector(1,n);    int   l1, l2;                         /* length counters */
   xicom=vector(1,n);  
   nrfunc=func;    l1 = strlen(path );                   /* length of path */
   for (j=1;j<=n;j++) {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     pcom[j]=p[j];    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     xicom[j]=xi[j];    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   }      strcpy( name, path );               /* we got the fullname name because no directory */
   ax=0.0;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   xx=1.0;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      /* get current working directory */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      /*    extern  char* getcwd ( char *buf , int len);*/
 #ifdef DEBUG      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);        return( GLOCK_ERROR_GETCWD );
 #endif      }
   for (j=1;j<=n;j++) {      /* got dirc from getcwd*/
     xi[j] *= xmin;      printf(" DIRC = %s \n",dirc);
     p[j] += xi[j];    } else {                              /* strip direcotry from path */
   }      ss++;                               /* after this, the filename */
   free_vector(xicom,1,n);      l2 = strlen( ss );                  /* length of filename */
   free_vector(pcom,1,n);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 }      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
 /*************** powell ************************/      dirc[l1-l2] = 0;                    /* add zero */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      printf(" DIRC2 = %s \n",dirc);
             double (*func)(double []))    }
 {    /* We add a separator at the end of dirc if not exists */
   void linmin(double p[], double xi[], int n, double *fret,    l1 = strlen( dirc );                  /* length of directory */
               double (*func)(double []));    if( dirc[l1-1] != DIRSEPARATOR ){
   int i,ibig,j;      dirc[l1] =  DIRSEPARATOR;
   double del,t,*pt,*ptt,*xit;      dirc[l1+1] = 0; 
   double fp,fptt;      printf(" DIRC3 = %s \n",dirc);
   double *xits;    }
   pt=vector(1,n);    ss = strrchr( name, '.' );            /* find last / */
   ptt=vector(1,n);    if (ss >0){
   xit=vector(1,n);      ss++;
   xits=vector(1,n);      strcpy(ext,ss);                     /* save extension */
   *fret=(*func)(p);      l1= strlen( name);
   for (j=1;j<=n;j++) pt[j]=p[j];      l2= strlen(ss)+1;
   for (*iter=1;;++(*iter)) {      strncpy( finame, name, l1-l2);
     fp=(*fret);      finame[l1-l2]= 0;
     ibig=0;    }
     del=0.0;  
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    return( 0 );                          /* we're done */
     for (i=1;i<=n;i++)  }
       printf(" %d %.12f",i, p[i]);  
     printf("\n");  
     for (i=1;i<=n;i++) {  /******************************************/
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  void replace_back_to_slash(char *s, char*t)
 #ifdef DEBUG  {
       printf("fret=%lf \n",*fret);    int i;
 #endif    int lg=0;
       printf("%d",i);fflush(stdout);    i=0;
       linmin(p,xit,n,fret,func);    lg=strlen(t);
       if (fabs(fptt-(*fret)) > del) {    for(i=0; i<= lg; i++) {
         del=fabs(fptt-(*fret));      (s[i] = t[i]);
         ibig=i;      if (t[i]== '\\') s[i]='/';
       }    }
 #ifdef DEBUG  }
       printf("%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {  int nbocc(char *s, char occ)
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  {
         printf(" x(%d)=%.12e",j,xit[j]);    int i,j=0;
       }    int lg=20;
       for(j=1;j<=n;j++)    i=0;
         printf(" p=%.12e",p[j]);    lg=strlen(s);
       printf("\n");    for(i=0; i<= lg; i++) {
 #endif    if  (s[i] == occ ) j++;
     }    }
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    return j;
 #ifdef DEBUG  }
       int k[2],l;  
       k[0]=1;  void cutv(char *u,char *v, char*t, char occ)
       k[1]=-1;  {
       printf("Max: %.12e",(*func)(p));    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       for (j=1;j<=n;j++)       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
         printf(" %.12e",p[j]);       gives u="abcedf" and v="ghi2j" */
       printf("\n");    int i,lg,j,p=0;
       for(l=0;l<=1;l++) {    i=0;
         for (j=1;j<=n;j++) {    for(j=0; j<=strlen(t)-1; j++) {
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
           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)));    lg=strlen(t);
       }    for(j=0; j<p; j++) {
 #endif      (u[j] = t[j]);
     }
        u[p]='\0';
       free_vector(xit,1,n);  
       free_vector(xits,1,n);     for(j=0; j<= lg; j++) {
       free_vector(ptt,1,n);      if (j>=(p+1))(v[j-p-1] = t[j]);
       free_vector(pt,1,n);    }
       return;  }
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  /********************** nrerror ********************/
     for (j=1;j<=n;j++) {  
       ptt[j]=2.0*p[j]-pt[j];  void nrerror(char error_text[])
       xit[j]=p[j]-pt[j];  {
       pt[j]=p[j];    fprintf(stderr,"ERREUR ...\n");
     }    fprintf(stderr,"%s\n",error_text);
     fptt=(*func)(ptt);    exit(EXIT_FAILURE);
     if (fptt < fp) {  }
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  /*********************** vector *******************/
       if (t < 0.0) {  double *vector(int nl, int nh)
         linmin(p,xit,n,fret,func);  {
         for (j=1;j<=n;j++) {    double *v;
           xi[j][ibig]=xi[j][n];    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
           xi[j][n]=xit[j];    if (!v) nrerror("allocation failure in vector");
         }    return v-nl+NR_END;
 #ifdef DEBUG  }
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  
         for(j=1;j<=n;j++)  /************************ free vector ******************/
           printf(" %.12e",xit[j]);  void free_vector(double*v, int nl, int nh)
         printf("\n");  {
 #endif    free((FREE_ARG)(v+nl-NR_END));
       }  }
     }  
   }  /************************ivector *******************************/
 }  int *ivector(long nl,long nh)
   {
 /**** Prevalence limit ****************/    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    if (!v) nrerror("allocation failure in ivector");
 {    return v-nl+NR_END;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  }
      matrix by transitions matrix until convergence is reached */  
   /******************free ivector **************************/
   int i, ii,j,k;  void free_ivector(int *v, long nl, long nh)
   double min, max, maxmin, maxmax,sumnew=0.;  {
   double **matprod2();    free((FREE_ARG)(v+nl-NR_END));
   double **out, cov[NCOVMAX], **pmij();  }
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */  /************************lvector *******************************/
   long *lvector(long nl,long nh)
   for (ii=1;ii<=nlstate+ndeath;ii++)  {
     for (j=1;j<=nlstate+ndeath;j++){    long *v;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     }    if (!v) nrerror("allocation failure in ivector");
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    return v-nl+NR_END;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  }
     newm=savm;  
     /* Covariates have to be included here again */  /******************free lvector **************************/
     cov[1]=1.;  void free_lvector(long *v, long nl, long nh)
     cov[2]=agefin;  {
     if (cptcovn>0){    free((FREE_ARG)(v+nl-NR_END));
       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]]);*/}  }
     }  
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  /******************* imatrix *******************************/
   int **imatrix(long nrl, long nrh, long ncl, long nch) 
     savm=oldm;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     oldm=newm;  { 
     maxmax=0.;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     for(j=1;j<=nlstate;j++){    int **m; 
       min=1.;    
       max=0.;    /* allocate pointers to rows */ 
       for(i=1; i<=nlstate; i++) {    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         sumnew=0;    if (!m) nrerror("allocation failure 1 in matrix()"); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    m += NR_END; 
         prlim[i][j]= newm[i][j]/(1-sumnew);    m -= nrl; 
         max=FMAX(max,prlim[i][j]);    
         min=FMIN(min,prlim[i][j]);    
       }    /* allocate rows and set pointers to them */ 
       maxmin=max-min;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       maxmax=FMAX(maxmax,maxmin);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     }    m[nrl] += NR_END; 
     if(maxmax < ftolpl){    m[nrl] -= ncl; 
       return prlim;    
     }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   }    
 }    /* return pointer to array of pointers to rows */ 
     return m; 
 /*************** transition probabilities **********/  } 
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  /****************** free_imatrix *************************/
 {  void free_imatrix(m,nrl,nrh,ncl,nch)
   double s1, s2;        int **m;
   /*double t34;*/        long nch,ncl,nrh,nrl; 
   int i,j,j1, nc, ii, jj;       /* free an int matrix allocated by imatrix() */ 
   { 
     for(i=1; i<= nlstate; i++){    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     for(j=1; j<i;j++){    free((FREE_ARG) (m+nrl-NR_END)); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  } 
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /******************* matrix *******************************/
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  double **matrix(long nrl, long nrh, long ncl, long nch)
       }  {
       ps[i][j]=s2;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    double **m;
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    if (!m) nrerror("allocation failure 1 in matrix()");
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    m += NR_END;
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    m -= nrl;
       }  
       ps[i][j]=s2;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   }    m[nrl] += NR_END;
   for(i=1; i<= nlstate; i++){    m[nrl] -= ncl;
      s1=0;  
     for(j=1; j<i; j++)    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       s1+=exp(ps[i][j]);    return m;
     for(j=i+1; j<=nlstate+ndeath; j++)    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       s1+=exp(ps[i][j]);     */
     ps[i][i]=1./(s1+1.);  }
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /*************************free matrix ************************/
     for(j=i+1; j<=nlstate+ndeath; j++)  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       ps[i][j]= exp(ps[i][j])*ps[i][i];  {
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   } /* end i */    free((FREE_ARG)(m+nrl-NR_END));
   }
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  /******************* ma3x *******************************/
       ps[ii][jj]=0;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       ps[ii][ii]=1;  {
     }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   }    double ***m;
   
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     for(jj=1; jj<= nlstate+ndeath; jj++){    if (!m) nrerror("allocation failure 1 in matrix()");
      printf("%lf ",ps[ii][jj]);    m += NR_END;
    }    m -= nrl;
     printf("\n ");  
     }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     printf("\n ");printf("%lf ",cov[2]);*/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 /*    m[nrl] += NR_END;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    m[nrl] -= ncl;
   goto end;*/  
     return ps;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 }  
     m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 /**************** Product of 2 matrices ******************/    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     m[nrl][ncl] += NR_END;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    m[nrl][ncl] -= nll;
 {    for (j=ncl+1; j<=nch; j++) 
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      m[nrl][j]=m[nrl][j-1]+nlay;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    
   /* in, b, out are matrice of pointers which should have been initialized    for (i=nrl+1; i<=nrh; i++) {
      before: only the contents of out is modified. The function returns      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
      a pointer to pointers identical to out */      for (j=ncl+1; j<=nch; j++) 
   long i, j, k;        m[i][j]=m[i][j-1]+nlay;
   for(i=nrl; i<= nrh; i++)    }
     for(k=ncolol; k<=ncoloh; k++)    return m; 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         out[i][k] +=in[i][j]*b[j][k];             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     */
   return out;  }
 }  
   /*************************free ma3x ************************/
   void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 /************* Higher Matrix Product ***************/  {
     free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 {    free((FREE_ARG)(m+nrl-NR_END));
   /* 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 subdirf ***********/
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  char *subdirf(char fileres[])
      (typically every 2 years instead of every month which is too big).  {
      Model is determined by parameters x and covariates have to be    /* Caution optionfilefiname is hidden */
      included manually here.    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
      */    strcat(tmpout,fileres);
     return tmpout;
   int i, j, d, h, k;  }
   double **out, cov[NCOVMAX];  
   double **newm;  /*************** function subdirf2 ***********/
   char *subdirf2(char fileres[], char *preop)
   /* Hstepm could be zero and should return the unit matrix */  {
   for (i=1;i<=nlstate+ndeath;i++)    
     for (j=1;j<=nlstate+ndeath;j++){    /* Caution optionfilefiname is hidden */
       oldm[i][j]=(i==j ? 1.0 : 0.0);    strcpy(tmpout,optionfilefiname);
       po[i][j][0]=(i==j ? 1.0 : 0.0);    strcat(tmpout,"/");
     }    strcat(tmpout,preop);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    strcat(tmpout,fileres);
   for(h=1; h <=nhstepm; h++){    return tmpout;
     for(d=1; d <=hstepm; d++){  }
       newm=savm;  
       /* Covariates have to be included here again */  /*************** function subdirf3 ***********/
       cov[1]=1.;  char *subdirf3(char fileres[], char *preop, char *preop2)
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  {
       if (cptcovn>0){    
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];    /* Caution optionfilefiname is hidden */
     }    strcpy(tmpout,optionfilefiname);
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    strcat(tmpout,"/");
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    strcat(tmpout,preop);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    strcat(tmpout,preop2);
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    strcat(tmpout,fileres);
       savm=oldm;    return tmpout;
       oldm=newm;  }
     }  
     for(i=1; i<=nlstate+ndeath; i++)  /***************** f1dim *************************/
       for(j=1;j<=nlstate+ndeath;j++) {  extern int ncom; 
         po[i][j][h]=newm[i][j];  extern double *pcom,*xicom;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  extern double (*nrfunc)(double []); 
          */   
       }  double f1dim(double x) 
   } /* end h */  { 
   return po;    int j; 
 }    double f;
     double *xt; 
    
 /*************** log-likelihood *************/    xt=vector(1,ncom); 
 double func( double *x)    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 {    f=(*nrfunc)(xt); 
   int i, ii, j, k, mi, d;    free_vector(xt,1,ncom); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    return f; 
   double **out;  } 
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */  /*****************brent *************************/
   long ipmx;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   /*extern weight */  { 
   /* We are differentiating ll according to initial status */    int iter; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    double a,b,d,etemp;
   /*for(i=1;i<imx;i++)    double fu,fv,fw,fx;
 printf(" %d\n",s[4][i]);    double ftemp;
   */    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     double e=0.0; 
   for(k=1; k<=nlstate; k++) ll[k]=0.;   
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    a=(ax < cx ? ax : cx); 
        for(mi=1; mi<= wav[i]-1; mi++){    b=(ax > cx ? ax : cx); 
       for (ii=1;ii<=nlstate+ndeath;ii++)    x=w=v=bx; 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    fw=fv=fx=(*f)(x); 
             for(d=0; d<dh[mi][i]; d++){    for (iter=1;iter<=ITMAX;iter++) { 
         newm=savm;      xm=0.5*(a+b); 
           cov[1]=1.;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
           if (cptcovn>0){      printf(".");fflush(stdout);
             for (k=1; k<=cptcovn;k++) {      fprintf(ficlog,".");fflush(ficlog);
               cov[2+k]=covar[Tvar[k]][i];  #ifdef DEBUG
               /* printf("k=%d cptcovn=%d %lf\n",k,cptcovn,covar[Tvar[k]][i]);*/      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
             }      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);
             }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  #endif
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
           savm=oldm;        *xmin=x; 
           oldm=newm;        return fx; 
       } /* end mult */      } 
          ftemp=fu;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      if (fabs(e) > tol1) { 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        r=(x-w)*(fx-fv); 
       ipmx +=1;        q=(x-v)*(fx-fw); 
       sw += weight[i];        p=(x-v)*q-(x-w)*r; 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        q=2.0*(q-r); 
     } /* end of wave */        if (q > 0.0) p = -p; 
   } /* end of individual */        q=fabs(q); 
         etemp=e; 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        e=d; 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         else { 
   return -l;          d=p/q; 
 }          u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
 /*********** Maximum Likelihood Estimation ***************/        } 
       } else { 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 {      } 
   int i,j, iter;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double **xi,*delti;      fu=(*f)(u); 
   double fret;      if (fu <= fx) { 
   xi=matrix(1,npar,1,npar);        if (u >= x) a=x; else b=x; 
   for (i=1;i<=npar;i++)        SHFT(v,w,x,u) 
     for (j=1;j<=npar;j++)          SHFT(fv,fw,fx,fu) 
       xi[i][j]=(i==j ? 1.0 : 0.0);          } else { 
   printf("Powell\n");            if (u < x) a=u; else b=u; 
   powell(p,xi,npar,ftol,&iter,&fret,func);            if (fu <= fw || w == x) { 
               v=w; 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));              w=u; 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));              fv=fw; 
               fw=fu; 
 }            } else if (fu <= fv || v == x || v == w) { 
               v=u; 
 /**** Computes Hessian and covariance matrix ***/              fv=fu; 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))            } 
 {          } 
   double  **a,**y,*x,pd;    } 
   double **hess;    nrerror("Too many iterations in brent"); 
   int i, j,jk;    *xmin=x; 
   int *indx;    return fx; 
   } 
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);  /****************** mnbrak ***********************/
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               double (*func)(double)) 
   { 
   hess=matrix(1,npar,1,npar);    double ulim,u,r,q, dum;
     double fu; 
   printf("\nCalculation of the hessian matrix. Wait...\n");   
   for (i=1;i<=npar;i++){    *fa=(*func)(*ax); 
     printf("%d",i);fflush(stdout);    *fb=(*func)(*bx); 
     hess[i][i]=hessii(p,ftolhess,i,delti);    if (*fb > *fa) { 
     /*printf(" %f ",p[i]);*/      SHFT(dum,*ax,*bx,dum) 
   }        SHFT(dum,*fb,*fa,dum) 
         } 
   for (i=1;i<=npar;i++) {    *cx=(*bx)+GOLD*(*bx-*ax); 
     for (j=1;j<=npar;j++)  {    *fc=(*func)(*cx); 
       if (j>i) {    while (*fb > *fc) { 
         printf(".%d%d",i,j);fflush(stdout);      r=(*bx-*ax)*(*fb-*fc); 
         hess[i][j]=hessij(p,delti,i,j);      q=(*bx-*cx)*(*fb-*fa); 
         hess[j][i]=hess[i][j];      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     }      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   }      if ((*bx-u)*(u-*cx) > 0.0) { 
   printf("\n");        fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        fu=(*func)(u); 
          if (fu < *fc) { 
   a=matrix(1,npar,1,npar);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   y=matrix(1,npar,1,npar);            SHFT(*fb,*fc,fu,(*func)(u)) 
   x=vector(1,npar);            } 
   indx=ivector(1,npar);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   for (i=1;i<=npar;i++)        u=ulim; 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        fu=(*func)(u); 
   ludcmp(a,npar,indx,&pd);      } else { 
         u=(*cx)+GOLD*(*cx-*bx); 
   for (j=1;j<=npar;j++) {        fu=(*func)(u); 
     for (i=1;i<=npar;i++) x[i]=0;      } 
     x[j]=1;      SHFT(*ax,*bx,*cx,u) 
     lubksb(a,npar,indx,x);        SHFT(*fa,*fb,*fc,fu) 
     for (i=1;i<=npar;i++){        } 
       matcov[i][j]=x[i];  } 
     }  
   }  /*************** linmin ************************/
   
   printf("\n#Hessian matrix#\n");  int ncom; 
   for (i=1;i<=npar;i++) {  double *pcom,*xicom;
     for (j=1;j<=npar;j++) {  double (*nrfunc)(double []); 
       printf("%.3e ",hess[i][j]);   
     }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     printf("\n");  { 
   }    double brent(double ax, double bx, double cx, 
                  double (*f)(double), double tol, double *xmin); 
   /* Recompute Inverse */    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++) a[i][j]=matcov[i][j];                double *fc, double (*func)(double)); 
   ludcmp(a,npar,indx,&pd);    int j; 
     double xx,xmin,bx,ax; 
   /*  printf("\n#Hessian matrix recomputed#\n");    double fx,fb,fa;
    
   for (j=1;j<=npar;j++) {    ncom=n; 
     for (i=1;i<=npar;i++) x[i]=0;    pcom=vector(1,n); 
     x[j]=1;    xicom=vector(1,n); 
     lubksb(a,npar,indx,x);    nrfunc=func; 
     for (i=1;i<=npar;i++){    for (j=1;j<=n;j++) { 
       y[i][j]=x[i];      pcom[j]=p[j]; 
       printf("%.3e ",y[i][j]);      xicom[j]=xi[j]; 
     }    } 
     printf("\n");    ax=0.0; 
   }    xx=1.0; 
   */    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   free_matrix(a,1,npar,1,npar);  #ifdef DEBUG
   free_matrix(y,1,npar,1,npar);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   free_vector(x,1,npar);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   free_ivector(indx,1,npar);  #endif
   free_matrix(hess,1,npar,1,npar);    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
       p[j] += xi[j]; 
 }    } 
     free_vector(xicom,1,n); 
 /*************** hessian matrix ****************/    free_vector(pcom,1,n); 
 double hessii( double x[], double delta, int theta, double delti[])  } 
 {  
   int i;  char *asc_diff_time(long time_sec, char ascdiff[])
   int l=1, lmax=20;  {
   double k1,k2;    long sec_left, days, hours, minutes;
   double p2[NPARMAX+1];    days = (time_sec) / (60*60*24);
   double res;    sec_left = (time_sec) % (60*60*24);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    hours = (sec_left) / (60*60) ;
   double fx;    sec_left = (sec_left) %(60*60);
   int k=0,kmax=10;    minutes = (sec_left) /60;
   double l1;    sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   fx=func(x);    return ascdiff;
   for (i=1;i<=npar;i++) p2[i]=x[i];  }
   for(l=0 ; l <=lmax; l++){  
     l1=pow(10,l);  /*************** powell ************************/
     delts=delt;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     for(k=1 ; k <kmax; k=k+1){              double (*func)(double [])) 
       delt = delta*(l1*k);  { 
       p2[theta]=x[theta] +delt;    void linmin(double p[], double xi[], int n, double *fret, 
       k1=func(p2)-fx;                double (*func)(double [])); 
       p2[theta]=x[theta]-delt;    int i,ibig,j; 
       k2=func(p2)-fx;    double del,t,*pt,*ptt,*xit;
       /*res= (k1-2.0*fx+k2)/delt/delt; */    double fp,fptt;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    double *xits;
          int niterf, itmp;
 #ifdef DEBUG  
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    pt=vector(1,n); 
 #endif    ptt=vector(1,n); 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    xit=vector(1,n); 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    xits=vector(1,n); 
         k=kmax;    *fret=(*func)(p); 
       }    for (j=1;j<=n;j++) pt[j]=p[j]; 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    for (*iter=1;;++(*iter)) { 
         k=kmax; l=lmax*10.;      fp=(*fret); 
       }      ibig=0; 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      del=0.0; 
         delts=delt;      last_time=curr_time;
       }      (void) gettimeofday(&curr_time,&tzp);
     }      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
   }      /*    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
   delti[theta]=delts;      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   return res;        */
 }     for (i=1;i<=n;i++) {
         printf(" %d %.12f",i, p[i]);
 double hessij( double x[], double delti[], int thetai,int thetaj)        fprintf(ficlog," %d %.12lf",i, p[i]);
 {        fprintf(ficrespow," %.12lf", p[i]);
   int i;      }
   int l=1, l1, lmax=20;      printf("\n");
   double k1,k2,k3,k4,res,fx;      fprintf(ficlog,"\n");
   double p2[NPARMAX+1];      fprintf(ficrespow,"\n");fflush(ficrespow);
   int k;      if(*iter <=3){
         tm = *localtime(&curr_time.tv_sec);
   fx=func(x);        strcpy(strcurr,asctime(&tm));
   for (k=1; k<=2; k++) {  /*       asctime_r(&tm,strcurr); */
     for (i=1;i<=npar;i++) p2[i]=x[i];        forecast_time=curr_time; 
     p2[thetai]=x[thetai]+delti[thetai]/k;        itmp = strlen(strcurr);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     k1=func(p2)-fx;          strcurr[itmp-1]='\0';
          printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     p2[thetai]=x[thetai]+delti[thetai]/k;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        for(niterf=10;niterf<=30;niterf+=10){
     k2=func(p2)-fx;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
            tmf = *localtime(&forecast_time.tv_sec);
     p2[thetai]=x[thetai]-delti[thetai]/k;  /*      asctime_r(&tmf,strfor); */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          strcpy(strfor,asctime(&tmf));
     k3=func(p2)-fx;          itmp = strlen(strfor);
            if(strfor[itmp-1]=='\n')
     p2[thetai]=x[thetai]-delti[thetai]/k;          strfor[itmp-1]='\0';
     p2[thetaj]=x[thetaj]-delti[thetaj]/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);
     k4=func(p2)-fx;          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);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        }
 #ifdef DEBUG      }
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);      for (i=1;i<=n;i++) { 
 #endif        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   }        fptt=(*fret); 
   return res;  #ifdef DEBUG
 }        printf("fret=%lf \n",*fret);
         fprintf(ficlog,"fret=%lf \n",*fret);
 /************** Inverse of matrix **************/  #endif
 void ludcmp(double **a, int n, int *indx, double *d)        printf("%d",i);fflush(stdout);
 {        fprintf(ficlog,"%d",i);fflush(ficlog);
   int i,imax,j,k;        linmin(p,xit,n,fret,func); 
   double big,dum,sum,temp;        if (fabs(fptt-(*fret)) > del) { 
   double *vv;          del=fabs(fptt-(*fret)); 
            ibig=i; 
   vv=vector(1,n);        } 
   *d=1.0;  #ifdef DEBUG
   for (i=1;i<=n;i++) {        printf("%d %.12e",i,(*fret));
     big=0.0;        fprintf(ficlog,"%d %.12e",i,(*fret));
     for (j=1;j<=n;j++)        for (j=1;j<=n;j++) {
       if ((temp=fabs(a[i][j])) > big) big=temp;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          printf(" x(%d)=%.12e",j,xit[j]);
     vv[i]=1.0/big;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   }        }
   for (j=1;j<=n;j++) {        for(j=1;j<=n;j++) {
     for (i=1;i<j;i++) {          printf(" p=%.12e",p[j]);
       sum=a[i][j];          fprintf(ficlog," p=%.12e",p[j]);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        }
       a[i][j]=sum;        printf("\n");
     }        fprintf(ficlog,"\n");
     big=0.0;  #endif
     for (i=j;i<=n;i++) {      } 
       sum=a[i][j];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       for (k=1;k<j;k++)  #ifdef DEBUG
         sum -= a[i][k]*a[k][j];        int k[2],l;
       a[i][j]=sum;        k[0]=1;
       if ( (dum=vv[i]*fabs(sum)) >= big) {        k[1]=-1;
         big=dum;        printf("Max: %.12e",(*func)(p));
         imax=i;        fprintf(ficlog,"Max: %.12e",(*func)(p));
       }        for (j=1;j<=n;j++) {
     }          printf(" %.12e",p[j]);
     if (j != imax) {          fprintf(ficlog," %.12e",p[j]);
       for (k=1;k<=n;k++) {        }
         dum=a[imax][k];        printf("\n");
         a[imax][k]=a[j][k];        fprintf(ficlog,"\n");
         a[j][k]=dum;        for(l=0;l<=1;l++) {
       }          for (j=1;j<=n;j++) {
       *d = -(*d);            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       vv[imax]=vv[j];            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]);
     indx[j]=imax;          }
     if (a[j][j] == 0.0) a[j][j]=TINY;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     if (j != n) {          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       dum=1.0/(a[j][j]);        }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  #endif
     }  
   }  
   free_vector(vv,1,n);  /* Doesn't work */        free_vector(xit,1,n); 
 ;        free_vector(xits,1,n); 
 }        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
 void lubksb(double **a, int n, int *indx, double b[])        return; 
 {      } 
   int i,ii=0,ip,j;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   double sum;      for (j=1;j<=n;j++) { 
          ptt[j]=2.0*p[j]-pt[j]; 
   for (i=1;i<=n;i++) {        xit[j]=p[j]-pt[j]; 
     ip=indx[i];        pt[j]=p[j]; 
     sum=b[ip];      } 
     b[ip]=b[i];      fptt=(*func)(ptt); 
     if (ii)      if (fptt < fp) { 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     else if (sum) ii=i;        if (t < 0.0) { 
     b[i]=sum;          linmin(p,xit,n,fret,func); 
   }          for (j=1;j<=n;j++) { 
   for (i=n;i>=1;i--) {            xi[j][ibig]=xi[j][n]; 
     sum=b[i];            xi[j][n]=xit[j]; 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          }
     b[i]=sum/a[i][i];  #ifdef DEBUG
   }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 }          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(j=1;j<=n;j++){
 /************ Frequencies ********************/            printf(" %.12e",xit[j]);
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)            fprintf(ficlog," %.12e",xit[j]);
 {  /* Some frequencies */          }
            printf("\n");
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          fprintf(ficlog,"\n");
   double ***freq; /* Frequencies */  #endif
   double *pp;        }
   double pos;      } 
   FILE *ficresp;    } 
   char fileresp[FILENAMELENGTH];  } 
   
   pp=vector(1,nlstate);  /**** Prevalence limit (stable or period prevalence)  ****************/
   
   strcpy(fileresp,"p");  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   strcat(fileresp,fileres);  {
   if((ficresp=fopen(fileresp,"w"))==NULL) {    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     printf("Problem with prevalence resultfile: %s\n", fileresp);       matrix by transitions matrix until convergence is reached */
     exit(0);  
   }    int i, ii,j,k;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    double min, max, maxmin, maxmax,sumnew=0.;
   j1=0;    double **matprod2();
     double **out, cov[NCOVMAX], **pmij();
   j=cptcovn;    double **newm;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    double agefin, delaymax=50 ; /* Max number of years to converge */
   
   for(k1=1; k1<=j;k1++){    for (ii=1;ii<=nlstate+ndeath;ii++)
    for(i1=1; i1<=ncodemax[k1];i1++){      for (j=1;j<=nlstate+ndeath;j++){
        j1++;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
         for (i=-1; i<=nlstate+ndeath; i++)    
          for (jk=-1; jk<=nlstate+ndeath; jk++)       cov[1]=1.;
            for(m=agemin; m <= agemax+3; m++)   
              freq[i][jk][m]=0;   /* 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 (i=1; i<=imx; i++) {      newm=savm;
          bool=1;      /* Covariates have to be included here again */
          if  (cptcovn>0) {       cov[2]=agefin;
            for (z1=1; z1<=cptcovn; z1++)    
              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;        for (k=1; k<=cptcovn;k++) {
          }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           if (bool==1) {          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
            for(m=firstpass; m<=lastpass-1; m++){        }
              if(agev[m][i]==0) agev[m][i]=agemax+1;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
              if(agev[m][i]==1) agev[m][i]=agemax+2;        for (k=1; k<=cptcovprod;k++)
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  
            }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
          }        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
        }        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
         if  (cptcovn>0) {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
          fprintf(ficresp, "\n#Variable");  
          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);      savm=oldm;
        }      oldm=newm;
        fprintf(ficresp, "\n#");      maxmax=0.;
        for(i=1; i<=nlstate;i++)      for(j=1;j<=nlstate;j++){
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        min=1.;
        fprintf(ficresp, "\n");        max=0.;
                for(i=1; i<=nlstate; i++) {
   for(i=(int)agemin; i <= (int)agemax+3; i++){          sumnew=0;
     if(i==(int)agemax+3)          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       printf("Total");          prlim[i][j]= newm[i][j]/(1-sumnew);
     else          max=FMAX(max,prlim[i][j]);
       printf("Age %d", i);          min=FMIN(min,prlim[i][j]);
     for(jk=1; jk <=nlstate ; jk++){        }
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        maxmin=max-min;
         pp[jk] += freq[jk][m][i];        maxmax=FMAX(maxmax,maxmin);
     }      }
     for(jk=1; jk <=nlstate ; jk++){      if(maxmax < ftolpl){
       for(m=-1, pos=0; m <=0 ; m++)        return prlim;
         pos += freq[jk][m][i];      }
       if(pp[jk]>=1.e-10)    }
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  }
       else  
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  /*************** transition probabilities ***************/ 
     }  
     for(jk=1; jk <=nlstate ; jk++){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)  {
         pp[jk] += freq[jk][m][i];    double s1, s2;
     }    /*double t34;*/
     for(jk=1,pos=0; jk <=nlstate ; jk++)    int i,j,j1, nc, ii, jj;
       pos += pp[jk];  
     for(jk=1; jk <=nlstate ; jk++){      for(i=1; i<= nlstate; i++){
       if(pos>=1.e-5)        for(j=1; j<i;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 += param[i][j][nc]*cov[nc];*/
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       if( i <= (int) agemax){  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
         if(pos>=1.e-5)          }
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          ps[i][j]=s2;
       else  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        }
       }        for(j=i+1; j<=nlstate+ndeath;j++){
     }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     for(jk=-1; jk <=nlstate+ndeath; jk++)            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       for(m=-1; m <=nlstate+ndeath; m++)  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          }
     if(i <= (int) agemax)          ps[i][j]=s2;
       fprintf(ficresp,"\n");        }
     printf("\n");      }
     }      /*ps[3][2]=1;*/
     }      
  }      for(i=1; i<= nlstate; i++){
          s1=0;
   fclose(ficresp);        for(j=1; j<i; j++)
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          s1+=exp(ps[i][j]);
   free_vector(pp,1,nlstate);        for(j=i+1; j<=nlstate+ndeath; j++)
           s1+=exp(ps[i][j]);
 }  /* End of Freq */        ps[i][i]=1./(s1+1.);
         for(j=1; j<i; j++)
 /************* Waves Concatenation ***************/          ps[i][j]= exp(ps[i][j])*ps[i][i];
         for(j=i+1; j<=nlstate+ndeath; j++)
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          ps[i][j]= exp(ps[i][j])*ps[i][i];
 {        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      } /* end i */
      Death is a valid wave (if date is known).      
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        for(jj=1; jj<= nlstate+ndeath; jj++){
      and mw[mi+1][i]. dh depends on stepm.          ps[ii][jj]=0;
      */          ps[ii][ii]=1;
         }
   int i, mi, m;      }
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      
 float sum=0.;  
   /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   for(i=1; i<=imx; i++){  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
     mi=0;  /*         printf("ddd %lf ",ps[ii][jj]); */
     m=firstpass;  /*       } */
     while(s[m][i] <= nlstate){  /*       printf("\n "); */
       if(s[m][i]>=1)  /*        } */
         mw[++mi][i]=m;  /*        printf("\n ");printf("%lf ",cov[2]); */
       if(m >=lastpass)         /*
         break;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       else        goto end;*/
         m++;      return ps;
     }/* end while */  }
     if (s[m][i] > nlstate){  
       mi++;     /* Death is another wave */  /**************** Product of 2 matrices ******************/
       /* if(mi==0)  never been interviewed correctly before death */  
          /* Only death is a correct wave */  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       mw[mi][i]=m;  {
     }    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
        b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     wav[i]=mi;    /* in, b, out are matrice of pointers which should have been initialized 
     if(mi==0)       before: only the contents of out is modified. The function returns
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);       a pointer to pointers identical to out */
   }    long i, j, k;
     for(i=nrl; i<= nrh; i++)
   for(i=1; i<=imx; i++){      for(k=ncolol; k<=ncoloh; k++)
     for(mi=1; mi<wav[i];mi++){        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       if (stepm <=0)          out[i][k] +=in[i][j]*b[j][k];
         dh[mi][i]=1;  
       else{    return out;
         if (s[mw[mi+1][i]][i] > nlstate) {  }
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  
           if(j=0) j=1;  /* Survives at least one month after exam */  
         }  /************* Higher Matrix Product ***************/
         else{  
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
           /*printf("i=%d agevi+1=%lf agevi=%lf j=%d\n", i,agev[mw[mi+1][i]][i],agev[mw[mi][i]][i],j);*/  {
     /* Computes the transition matrix starting at age 'age' over 
           k=k+1;       'nhstepm*hstepm*stepm' months (i.e. until
           if (j >= jmax) jmax=j;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
           else if (j <= jmin)jmin=j;       nhstepm*hstepm matrices. 
           sum=sum+j;       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 
         jk= j/stepm;       for the memory).
         jl= j -jk*stepm;       Model is determined by parameters x and covariates have to be 
         ju= j -(jk+1)*stepm;       included manually here. 
         if(jl <= -ju)  
           dh[mi][i]=jk;       */
         else  
           dh[mi][i]=jk+1;    int i, j, d, h, k;
         if(dh[mi][i]==0)    double **out, cov[NCOVMAX];
           dh[mi][i]=1; /* At least one step */    double **newm;
       }  
     }    /* Hstepm could be zero and should return the unit matrix */
   }    for (i=1;i<=nlstate+ndeath;i++)
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);      for (j=1;j<=nlstate+ndeath;j++){
 }        oldm[i][j]=(i==j ? 1.0 : 0.0);
 /*********** Tricode ****************************/        po[i][j][0]=(i==j ? 1.0 : 0.0);
 void tricode(int *Tvar, int **nbcode, int imx)      }
 {    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   int Ndum[80],ij, k, j, i;    for(h=1; h <=nhstepm; h++){
   int cptcode=0;      for(d=1; d <=hstepm; d++){
   for (k=0; k<79; k++) Ndum[k]=0;        newm=savm;
   for (k=1; k<=7; k++) ncodemax[k]=0;        /* Covariates have to be included here again */
          cov[1]=1.;
   for (j=1; j<=cptcovn; j++) {        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     for (i=1; i<=imx; i++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       ij=(int)(covar[Tvar[j]][i]);        for (k=1; k<=cptcovage;k++)
       Ndum[ij]++;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       if (ij > cptcode) cptcode=ij;        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]]];
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/  
     for (i=0; i<=cptcode; i++) {  
       if(Ndum[i]!=0) ncodemax[j]++;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     }        /*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, 
     ij=1;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (i=1; i<=ncodemax[j]; i++) {        savm=oldm;
       for (k=0; k<=79; k++) {        oldm=newm;
         if (Ndum[k] != 0) {      }
           nbcode[Tvar[j]][ij]=k;      for(i=1; i<=nlstate+ndeath; i++)
           ij++;        for(j=1;j<=nlstate+ndeath;j++) {
         }          po[i][j][h]=newm[i][j];
         if (ij > ncodemax[j]) break;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       }             */
     }        }
   }      } /* end h */
     return po;
   }  }
   
 /*********** Health Expectancies ****************/  
   /*************** log-likelihood *************/
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)  double func( double *x)
 {  {
   /* Health expectancies */    int i, ii, j, k, mi, d, kk;
   int i, j, nhstepm, hstepm, h;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   double age, agelim,hf;    double **out;
   double ***p3mat;    double sw; /* Sum of weights */
      double lli; /* Individual log likelihood */
   fprintf(ficreseij,"# Health expectancies\n");    int s1, s2;
   fprintf(ficreseij,"# Age");    double bbh, survp;
   for(i=1; i<=nlstate;i++)    long ipmx;
     for(j=1; j<=nlstate;j++)    /*extern weight */
       fprintf(ficreseij," %1d-%1d",i,j);    /* We are differentiating ll according to initial status */
   fprintf(ficreseij,"\n");    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
   hstepm=1*YEARM; /*  Every j years of age (in month) */      printf(" %d\n",s[4][i]);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    */
     cov[1]=1.;
   agelim=AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    for(k=1; k<=nlstate; k++) ll[k]=0.;
     /* nhstepm age range expressed in number of stepm */  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);    if(mle==1){
     /* Typically if 20 years = 20*12/6=40 stepm */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     if (stepm >= YEARM) hstepm=1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */        for(mi=1; mi<= wav[i]-1; mi++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (ii=1;ii<=nlstate+ndeath;ii++)
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            for (j=1;j<=nlstate+ndeath;j++){
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
           for(d=0; d<dh[mi][i]; d++){
     for(i=1; i<=nlstate;i++)            newm=savm;
       for(j=1; j<=nlstate;j++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){            for (kk=1; kk<=cptcovage;kk++) {
           eij[i][j][(int)age] +=p3mat[i][j][h];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }            }
                out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     hf=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     if (stepm >= YEARM) hf=stepm/YEARM;            savm=oldm;
     fprintf(ficreseij,"%.0f",age );            oldm=newm;
     for(i=1; i<=nlstate;i++)          } /* end mult */
       for(j=1; j<=nlstate;j++){        
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          /*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.
     fprintf(ficreseij,"\n");           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           * (in months) between two waves is not a multiple of stepm, we rounded to 
   }           * the nearest (and in case of equal distance, to the lowest) interval but now
 }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
 /************ Variance ******************/           * probability in order to take into account the bias as a fraction of the way
 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)           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
 {           * -stepm/2 to stepm/2 .
   /* Variance of health expectancies */           * For stepm=1 the results are the same as for previous versions of Imach.
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/           * For stepm > 1 the results are less biased than in previous versions. 
   double **newm;           */
   double **dnewm,**doldm;          s1=s[mw[mi][i]][i];
   int i, j, nhstepm, hstepm, h;          s2=s[mw[mi+1][i]][i];
   int k, cptcode;          bbh=(double)bh[mi][i]/(double)stepm; 
    double *xp;          /* bias bh is positive if real duration
   double **gp, **gm;           * is higher than the multiple of stepm and negative otherwise.
   double ***gradg, ***trgradg;           */
   double ***p3mat;          /* 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 age,agelim;          if( s2 > nlstate){ 
   int theta;            /* i.e. if s2 is a death state and if the date of death is known 
                then the contribution to the likelihood is the probability to 
    fprintf(ficresvij,"# Covariances of life expectancies\n");               die between last step unit time and current  step unit time, 
   fprintf(ficresvij,"# Age");               which is also equal to probability to die before dh 
   for(i=1; i<=nlstate;i++)               minus probability to die before dh-stepm . 
     for(j=1; j<=nlstate;j++)               In version up to 0.92 likelihood was computed
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          as if date of death was unknown. Death was treated as any other
   fprintf(ficresvij,"\n");          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
   xp=vector(1,npar);          to consider that at each interview the state was recorded
   dnewm=matrix(1,nlstate,1,npar);          (healthy, disable or death) and IMaCh was corrected; but when we
   doldm=matrix(1,nlstate,1,nlstate);          introduced the exact date of death then we should have modified
            the contribution of an exact death to the likelihood. This new
   hstepm=1*YEARM; /* Every year of age */          contribution is smaller and very dependent of the step unit
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          stepm. It is no more the probability to die between last interview
   agelim = AGESUP;          and month of death but the probability to survive from last
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          interview up to one month before death multiplied by the
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          probability to die within a month. Thanks to Chris
     if (stepm >= YEARM) hstepm=1;          Jackson for correcting this bug.  Former versions increased
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          mortality artificially. The bad side is that we add another loop
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          which slows down the processing. The difference can be up to 10%
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          lower mortality.
     gp=matrix(0,nhstepm,1,nlstate);            */
     gm=matrix(0,nhstepm,1,nlstate);            lli=log(out[s1][s2] - savm[s1][s2]);
   
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */          } else if  (s2==-2) {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            for (j=1,survp=0. ; j<=nlstate; j++) 
       }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              /*survp += out[s1][j]; */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            lli= log(survp);
       for(j=1; j<= nlstate; j++){          }
         for(h=0; h<=nhstepm; h++){          
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          else if  (s2==-4) { 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            for (j=3,survp=0. ; j<=nlstate; j++)  
         }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       }            lli= log(survp); 
              } 
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          else if  (s2==-5) { 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              for (j=1,survp=0. ; j<=2; j++)  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       for(j=1; j<= nlstate; j++){            lli= log(survp); 
         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];          else{
         }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
       for(j=1; j<= nlstate; j++)          } 
         for(h=0; h<=nhstepm; h++){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          /*if(lli ==000.0)*/
         }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     } /* End theta */          ipmx +=1;
           sw += weight[i];
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
     for(h=0; h<=nhstepm; h++)      } /* end of individual */
       for(j=1; j<=nlstate;j++)    }  else if(mle==2){
         for(theta=1; theta <=npar; theta++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           trgradg[h][j][theta]=gradg[h][theta][j];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
     for(i=1;i<=nlstate;i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(j=1;j<=nlstate;j++)            for (j=1;j<=nlstate+ndeath;j++){
         vareij[i][j][(int)age] =0.;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(h=0;h<=nhstepm;h++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(k=0;k<=nhstepm;k++){            }
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          for(d=0; d<=dh[mi][i]; d++){
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            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] += doldm[i][j];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
     }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     h=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     if (stepm >= YEARM) h=stepm/YEARM;            savm=oldm;
     fprintf(ficresvij,"%.0f ",age );            oldm=newm;
     for(i=1; i<=nlstate;i++)          } /* end mult */
       for(j=1; j<=nlstate;j++){        
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);          s1=s[mw[mi][i]][i];
       }          s2=s[mw[mi+1][i]][i];
     fprintf(ficresvij,"\n");          bbh=(double)bh[mi][i]/(double)stepm; 
     free_matrix(gp,0,nhstepm,1,nlstate);          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 */
     free_matrix(gm,0,nhstepm,1,nlstate);          ipmx +=1;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          sw += weight[i];
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        } /* end of wave */
   } /* End age */      } /* end of individual */
      }  else if(mle==3){  /* exponential inter-extrapolation */
   free_vector(xp,1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_matrix(doldm,1,nlstate,1,npar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   free_matrix(dnewm,1,nlstate,1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
 }            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 /************ Variance of prevlim ******************/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)            }
 {          for(d=0; d<dh[mi][i]; d++){
   /* Variance of prevalence limit */            newm=savm;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double **newm;            for (kk=1; kk<=cptcovage;kk++) {
   double **dnewm,**doldm;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int i, j, nhstepm, hstepm;            }
   int k, cptcode;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double *xp;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double *gp, *gm;            savm=oldm;
   double **gradg, **trgradg;            oldm=newm;
   double age,agelim;          } /* end mult */
   int theta;        
              s1=s[mw[mi][i]][i];
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          s2=s[mw[mi+1][i]][i];
   fprintf(ficresvpl,"# Age");          bbh=(double)bh[mi][i]/(double)stepm; 
   for(i=1; i<=nlstate;i++)          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       fprintf(ficresvpl," %1d-%1d",i,i);          ipmx +=1;
   fprintf(ficresvpl,"\n");          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   xp=vector(1,npar);        } /* end of wave */
   dnewm=matrix(1,nlstate,1,npar);      } /* end of individual */
   doldm=matrix(1,nlstate,1,nlstate);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   hstepm=1*YEARM; /* Every year of age */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        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=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (stepm >= YEARM) hstepm=1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            }
     gradg=matrix(1,npar,1,nlstate);          for(d=0; d<dh[mi][i]; d++){
     gp=vector(1,nlstate);            newm=savm;
     gm=vector(1,nlstate);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     for(theta=1; theta <=npar; theta++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(i=1; i<=npar; i++){ /* Computes gradient */            }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          
       }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(i=1;i<=nlstate;i++)            savm=oldm;
         gp[i] = prlim[i][i];            oldm=newm;
              } /* 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];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          s2=s[mw[mi+1][i]][i];
       for(i=1;i<=nlstate;i++)          if( s2 > nlstate){ 
         gm[i] = prlim[i][i];            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
       for(i=1;i<=nlstate;i++)            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          }
     } /* End theta */          ipmx +=1;
           sw += weight[i];
     trgradg =matrix(1,nlstate,1,npar);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     for(j=1; j<=nlstate;j++)        } /* end of wave */
       for(theta=1; theta <=npar; theta++)      } /* end of individual */
         trgradg[j][theta]=gradg[theta][j];    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(i=1;i<=nlstate;i++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       varpl[i][(int)age] =0.;        for(mi=1; mi<= wav[i]-1; mi++){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          for (ii=1;ii<=nlstate+ndeath;ii++)
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);            for (j=1;j<=nlstate+ndeath;j++){
     for(i=1;i<=nlstate;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
     fprintf(ficresvpl,"%.0f ",age );          for(d=0; d<dh[mi][i]; d++){
     for(i=1; i<=nlstate;i++)            newm=savm;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     fprintf(ficresvpl,"\n");            for (kk=1; kk<=cptcovage;kk++) {
     free_vector(gp,1,nlstate);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     free_vector(gm,1,nlstate);            }
     free_matrix(gradg,1,npar,1,nlstate);          
     free_matrix(trgradg,1,nlstate,1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   } /* End age */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   free_vector(xp,1,npar);            oldm=newm;
   free_matrix(doldm,1,nlstate,1,npar);          } /* end mult */
   free_matrix(dnewm,1,nlstate,1,nlstate);        
           s1=s[mw[mi][i]][i];
 }          s2=s[mw[mi+1][i]][i];
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
           sw += weight[i];
 /***********************************************/          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /**************** Main Program *****************/          /*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 */
 /*int main(int argc, char *argv[])*/    } /* End of if */
 int main()    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 */
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;    return -l;
   double agedeb, agefin,hf;  }
   double agemin=1.e20, agemax=-1.e20;  
   /*************** log-likelihood *************/
   double fret;  double funcone( double *x)
   double **xi,tmp,delta;  {
     /* Same as likeli but slower because of a lot of printf and if */
   double dum; /* Dummy variable */    int i, ii, j, k, mi, d, kk;
   double ***p3mat;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   int *indx;    double **out;
   char line[MAXLINE], linepar[MAXLINE];    double lli; /* Individual log likelihood */
   char title[MAXLINE];    double llt;
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    int s1, s2;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];    double bbh, survp;
   char filerest[FILENAMELENGTH];    /*extern weight */
   char fileregp[FILENAMELENGTH];    /* We are differentiating ll according to initial status */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   int firstobs=1, lastobs=10;    /*for(i=1;i<imx;i++) 
   int sdeb, sfin; /* Status at beginning and end */      printf(" %d\n",s[4][i]);
   int c,  h , cpt,l;    */
   int ju,jl, mi;    cov[1]=1.;
   int i1,j1, k1,jk,aa,bb, stepsize;  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    for(k=1; k<=nlstate; k++) ll[k]=0.;
    
   int hstepm, nhstepm;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double bage, fage, age, agelim, agebase;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double ftolpl=FTOL;      for(mi=1; mi<= wav[i]-1; mi++){
   double **prlim;        for (ii=1;ii<=nlstate+ndeath;ii++)
   double *severity;          for (j=1;j<=nlstate+ndeath;j++){
   double ***param; /* Matrix of parameters */            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double  *p;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **matcov; /* Matrix of covariance */          }
   double ***delti3; /* Scale */        for(d=0; d<dh[mi][i]; d++){
   double *delti; /* Scale */          newm=savm;
   double ***eij, ***vareij;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double **varpl; /* Variances of prevalence limits by age */          for (kk=1; kk<=cptcovage;kk++) {
   double *epj, vepp;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";          }
   char *alph[]={"a","a","b","c","d","e"}, str[4];          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   char z[1]="c", occ;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 #include <sys/time.h>          savm=oldm;
 #include <time.h>          oldm=newm;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        } /* end mult */
   /* long total_usecs;        
   struct timeval start_time, end_time;        s1=s[mw[mi][i]][i];
          s2=s[mw[mi+1][i]][i];
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.
   printf("\nIMACH, Version 0.63");         */
   printf("\nEnter the parameter file name: ");        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
 #ifdef windows        } else if  (s2==-2) {
   scanf("%s",pathtot);          for (j=1,survp=0. ; j<=nlstate; j++) 
   getcwd(pathcd, size);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   cutv(path,optionfile,pathtot,'\\');          lli= log(survp);
   chdir(path);        }else if (mle==1){
   replace(pathc,path);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 #endif        } else if(mle==2){
 #ifdef unix          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",optionfile);        } else if(mle==3){  /* exponential inter-extrapolation */
 #endif          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         } else if (mle==4){  /* mle=4 no inter-extrapolation */
 /*-------- arguments in the command line --------*/          lli=log(out[s1][s2]); /* Original formula */
         } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   strcpy(fileres,"r");          lli=log(out[s1][s2]); /* Original formula */
   strcat(fileres, optionfile);        } /* End of if */
         ipmx +=1;
   /*---------arguments file --------*/        sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  /*       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("Problem with optionfile %s\n",optionfile);        if(globpr){
     goto end;          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   }   %11.6f %11.6f %11.6f ", \
                   num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   strcpy(filereso,"o");                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   strcat(filereso,fileres);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   if((ficparo=fopen(filereso,"w"))==NULL) {            llt +=ll[k]*gipmx/gsw;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   }          }
           fprintf(ficresilk," %10.6f\n", -llt);
   /* Reads comments: lines beginning with '#' */        }
   while((c=getc(ficpar))=='#' && c!= EOF){      } /* end of wave */
     ungetc(c,ficpar);    } /* end of individual */
     fgets(line, MAXLINE, ficpar);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     puts(line);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     fputs(line,ficparo);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   }    if(globpr==0){ /* First time we count the contributions and weights */
   ungetc(c,ficpar);      gipmx=ipmx;
       gsw=sw;
   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);    }
   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);    return -l;
   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);  }
   
   covar=matrix(1,NCOVMAX,1,n);      
   if (strlen(model)<=1) cptcovn=0;  /*************** function likelione ***********/
   else {  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     j=0;  {
     j=nbocc(model,'+');    /* This routine should help understanding what is done with 
     cptcovn=j+1;       the selection of individuals/waves and
   }       to check the exact contribution to the likelihood.
        Plotting could be done.
   ncovmodel=2+cptcovn;     */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    int k;
    
   /* Read guess parameters */    if(*globpri !=0){ /* Just counts and sums, no printings */
   /* Reads comments: lines beginning with '#' */      strcpy(fileresilk,"ilk"); 
   while((c=getc(ficpar))=='#' && c!= EOF){      strcat(fileresilk,fileres);
     ungetc(c,ficpar);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     fgets(line, MAXLINE, ficpar);        printf("Problem with resultfile: %s\n", fileresilk);
     puts(line);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     fputs(line,ficparo);      }
   }      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");
   ungetc(c,ficpar);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
        /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      for(k=1; k<=nlstate; k++) 
     for(i=1; i <=nlstate; i++)        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     for(j=1; j <=nlstate+ndeath-1; j++){      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       fscanf(ficpar,"%1d%1d",&i1,&j1);    }
       fprintf(ficparo,"%1d%1d",i1,j1);  
       printf("%1d%1d",i,j);    *fretone=(*funcone)(p);
       for(k=1; k<=ncovmodel;k++){    if(*globpri !=0){
         fscanf(ficpar," %lf",&param[i][j][k]);      fclose(ficresilk);
         printf(" %lf",param[i][j][k]);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
         fprintf(ficparo," %lf",param[i][j][k]);      fflush(fichtm); 
       }    } 
       fscanf(ficpar,"\n");    return;
       printf("\n");  }
       fprintf(ficparo,"\n");  
     }  
    /*********** Maximum Likelihood Estimation ***************/
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  
   p=param[1][1];  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
    {
   /* Reads comments: lines beginning with '#' */    int i,j, iter;
   while((c=getc(ficpar))=='#' && c!= EOF){    double **xi;
     ungetc(c,ficpar);    double fret;
     fgets(line, MAXLINE, ficpar);    double fretone; /* Only one call to likelihood */
     puts(line);    /*  char filerespow[FILENAMELENGTH];*/
     fputs(line,ficparo);    xi=matrix(1,npar,1,npar);
   }    for (i=1;i<=npar;i++)
   ungetc(c,ficpar);      for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    strcpy(filerespow,"pow"); 
   for(i=1; i <=nlstate; i++){    strcat(filerespow,fileres);
     for(j=1; j <=nlstate+ndeath-1; j++){    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       fscanf(ficpar,"%1d%1d",&i1,&j1);      printf("Problem with resultfile: %s\n", filerespow);
       printf("%1d%1d",i,j);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       fprintf(ficparo,"%1d%1d",i1,j1);    }
       for(k=1; k<=ncovmodel;k++){    fprintf(ficrespow,"# Powell\n# iter -2*LL");
         fscanf(ficpar,"%le",&delti3[i][j][k]);    for (i=1;i<=nlstate;i++)
         printf(" %le",delti3[i][j][k]);      for(j=1;j<=nlstate+ndeath;j++)
         fprintf(ficparo," %le",delti3[i][j][k]);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       }    fprintf(ficrespow,"\n");
       fscanf(ficpar,"\n");  
       printf("\n");    powell(p,xi,npar,ftol,&iter,&fret,func);
       fprintf(ficparo,"\n");  
     }    free_matrix(xi,1,npar,1,npar);
   }    fclose(ficrespow);
   delti=delti3[1][1];    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
      fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   /* Reads comments: lines beginning with '#' */    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  }
     fgets(line, MAXLINE, ficpar);  
     puts(line);  /**** Computes Hessian and covariance matrix ***/
     fputs(line,ficparo);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   }  {
   ungetc(c,ficpar);    double  **a,**y,*x,pd;
      double **hess;
   matcov=matrix(1,npar,1,npar);    int i, j,jk;
   for(i=1; i <=npar; i++){    int *indx;
     fscanf(ficpar,"%s",&str);  
     printf("%s",str);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     fprintf(ficparo,"%s",str);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     for(j=1; j <=i; j++){    void lubksb(double **a, int npar, int *indx, double b[]) ;
       fscanf(ficpar," %le",&matcov[i][j]);    void ludcmp(double **a, int npar, int *indx, double *d) ;
       printf(" %.5le",matcov[i][j]);    double gompertz(double p[]);
       fprintf(ficparo," %.5le",matcov[i][j]);    hess=matrix(1,npar,1,npar);
     }  
     fscanf(ficpar,"\n");    printf("\nCalculation of the hessian matrix. Wait...\n");
     printf("\n");    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficparo,"\n");    for (i=1;i<=npar;i++){
   }      printf("%d",i);fflush(stdout);
   for(i=1; i <=npar; i++)      fprintf(ficlog,"%d",i);fflush(ficlog);
     for(j=i+1;j<=npar;j++)     
       matcov[i][j]=matcov[j][i];       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
          
   printf("\n");      /*  printf(" %f ",p[i]);
           printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }
    if(mle==1){    
     /*-------- data file ----------*/    for (i=1;i<=npar;i++) {
     if((ficres =fopen(fileres,"w"))==NULL) {      for (j=1;j<=npar;j++)  {
       printf("Problem with resultfile: %s\n", fileres);goto end;        if (j>i) { 
     }          printf(".%d%d",i,j);fflush(stdout);
     fprintf(ficres,"#%s\n",version);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
              hess[i][j]=hessij(p,delti,i,j,func,npar);
     if((fic=fopen(datafile,"r"))==NULL)    {          
       printf("Problem with datafile: %s\n", datafile);goto end;          hess[j][i]=hess[i][j];    
     }          /*printf(" %lf ",hess[i][j]);*/
         }
     n= lastobs;      }
     severity = vector(1,maxwav);    }
     outcome=imatrix(1,maxwav+1,1,n);    printf("\n");
     num=ivector(1,n);    fprintf(ficlog,"\n");
     moisnais=vector(1,n);  
     annais=vector(1,n);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     moisdc=vector(1,n);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     andc=vector(1,n);    
     agedc=vector(1,n);    a=matrix(1,npar,1,npar);
     cod=ivector(1,n);    y=matrix(1,npar,1,npar);
     weight=vector(1,n);    x=vector(1,npar);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    indx=ivector(1,npar);
     mint=matrix(1,maxwav,1,n);    for (i=1;i<=npar;i++)
     anint=matrix(1,maxwav,1,n);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     s=imatrix(1,maxwav+1,1,n);    ludcmp(a,npar,indx,&pd);
     adl=imatrix(1,maxwav+1,1,n);      
     tab=ivector(1,NCOVMAX);    for (j=1;j<=npar;j++) {
     ncodemax=ivector(1,NCOVMAX);      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
     i=1;      lubksb(a,npar,indx,x);
     while (fgets(line, MAXLINE, fic) != NULL)    {      for (i=1;i<=npar;i++){ 
       if ((i >= firstobs) && (i <=lastobs)) {        matcov[i][j]=x[i];
              }
         for (j=maxwav;j>=1;j--){    }
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  
           strcpy(line,stra);    printf("\n#Hessian matrix#\n");
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficlog,"\n#Hessian matrix#\n");
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    for (i=1;i<=npar;i++) { 
         }      for (j=1;j<=npar;j++) { 
                printf("%.3e ",hess[i][j]);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficlog,"%.3e ",hess[i][j]);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      }
       printf("\n");
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      fprintf(ficlog,"\n");
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    }
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    /* Recompute Inverse */
         for (j=ncov;j>=1;j--){    for (i=1;i<=npar;i++)
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         }    ludcmp(a,npar,indx,&pd);
         num[i]=atol(stra);  
     /*  printf("\n#Hessian matrix recomputed#\n");
         /* printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/  
     for (j=1;j<=npar;j++) {
         /*printf("%d %.lf %.lf %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),(covar[3][i]), (covar[4][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]));*/      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
         i=i+1;      lubksb(a,npar,indx,x);
       }      for (i=1;i<=npar;i++){ 
     }        y[i][j]=x[i];
     /*scanf("%d",i);*/        printf("%.3e ",y[i][j]);
         fprintf(ficlog,"%.3e ",y[i][j]);
   imx=i-1; /* Number of individuals */      }
        printf("\n");
   /* Calculation of the number of parameter from char model*/      fprintf(ficlog,"\n");
   Tvar=ivector(1,8);        }
        */
   if (strlen(model) >1){  
     j=0;    free_matrix(a,1,npar,1,npar);
     j=nbocc(model,'+');    free_matrix(y,1,npar,1,npar);
     cptcovn=j+1;    free_vector(x,1,npar);
      free_ivector(indx,1,npar);
     strcpy(modelsav,model);    free_matrix(hess,1,npar,1,npar);
     if (j==0) {  
       cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb);  
     }  }
     else {  
       for(i=j; i>=1;i--){  /*************** hessian matrix ****************/
         cutv(stra,strb,modelsav,'+');  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
         if (strchr(strb,'*')) {  {
           cutv(strd,strc,strb,'*');    int i;
           cutv(strb,stre,strc,'V');Tvar[i+1]=ncov+1;    int l=1, lmax=20;
           cutv(strb,strc,strd,'V');    double k1,k2;
           for (k=1; k<=lastobs;k++)    double p2[NPARMAX+1];
             covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    double res;
         }    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         else {    double fx;
           cutv(strd,strc,strb,'V');    int k=0,kmax=10;
           Tvar[i+1]=atoi(strc);    double l1;
         }  
         strcpy(modelsav,stra);      fx=func(x);
       }    for (i=1;i<=npar;i++) p2[i]=x[i];
       /*cutv(strd,strc,stra,'V');*/    for(l=0 ; l <=lmax; l++){
       Tvar[1]=atoi(strc);      l1=pow(10,l);
     }      delts=delt;
   }      for(k=1 ; k <kmax; k=k+1){
   /*printf("tvar=%d ",Tvar[1]);*/        delt = delta*(l1*k);
   /*scanf("%d ",i);*/        p2[theta]=x[theta] +delt;
     fclose(fic);        k1=func(p2)-fx;
         p2[theta]=x[theta]-delt;
     if (weightopt != 1) { /* Maximisation without weights*/        k2=func(p2)-fx;
       for(i=1;i<=n;i++) weight[i]=1.0;        /*res= (k1-2.0*fx+k2)/delt/delt; */
     }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     /*-calculation of age at interview from date of interview and age at death -*/        
     agev=matrix(1,maxwav,1,imx);  #ifdef DEBUG
            printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     for (i=1; i<=imx; i++)  {        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);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  #endif
       for(m=1; (m<= maxwav); m++){        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if (mint[m][i]==99 || anint[m][i]==9999) s[m][i]=-1;          if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         if(s[m][i] >0){          k=kmax;
           if (s[m][i] == nlstate+1) {        }
             if(agedc[i]>0)        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
               if(moisdc[i]!=99 && andc[i]!=9999)          k=kmax; l=lmax*10.;
               agev[m][i]=agedc[i];        }
             else{        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);          delts=delt;
               agev[m][i]=-1;        }
             }      }
           }    }
           else if(s[m][i] !=9){ /* Should no more exist */    delti[theta]=delts;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    return res; 
             if(mint[m][i]==99 || anint[m][i]==9999){    
               agev[m][i]=1;  }
               /* printf("i=%d m=%d agev=%lf \n",i,m, agev[m][i]);    */  
             }  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
             else if(agev[m][i] <agemin){  {
               agemin=agev[m][i];    int i;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    int l=1, l1, lmax=20;
             }    double k1,k2,k3,k4,res,fx;
             else if(agev[m][i] >agemax){    double p2[NPARMAX+1];
               agemax=agev[m][i];    int k;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  
             }    fx=func(x);
             /*agev[m][i]=anint[m][i]-annais[i];*/    for (k=1; k<=2; k++) {
             /*   agev[m][i] = age[i]+2*m;*/      for (i=1;i<=npar;i++) p2[i]=x[i];
           }      p2[thetai]=x[thetai]+delti[thetai]/k;
           else { /* =9 */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
             agev[m][i]=1;      k1=func(p2)-fx;
             s[m][i]=-1;    
           }      p2[thetai]=x[thetai]+delti[thetai]/k;
         }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         else /*= 0 Unknown */      k2=func(p2)-fx;
           agev[m][i]=1;    
       }      p2[thetai]=x[thetai]-delti[thetai]/k;
          p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     }      k3=func(p2)-fx;
     for (i=1; i<=imx; i++)  {    
       for(m=1; (m<= maxwav); m++){      p2[thetai]=x[thetai]-delti[thetai]/k;
         if (s[m][i] > (nlstate+ndeath)) {      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           printf("Error: Wrong value in nlstate or ndeath\n");        k4=func(p2)-fx;
           goto end;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         }  #ifdef DEBUG
       }      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     }      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   #endif
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    }
     return res;
     free_vector(severity,1,maxwav);  }
     free_imatrix(outcome,1,maxwav+1,1,n);  
     free_vector(moisnais,1,n);  /************** Inverse of matrix **************/
     free_vector(annais,1,n);  void ludcmp(double **a, int n, int *indx, double *d) 
     free_matrix(mint,1,maxwav,1,n);  { 
     free_matrix(anint,1,maxwav,1,n);    int i,imax,j,k; 
     free_vector(moisdc,1,n);    double big,dum,sum,temp; 
     free_vector(andc,1,n);    double *vv; 
    
        vv=vector(1,n); 
     wav=ivector(1,imx);    *d=1.0; 
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    for (i=1;i<=n;i++) { 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      big=0.0; 
          for (j=1;j<=n;j++) 
     /* Concatenates waves */        if ((temp=fabs(a[i][j])) > big) big=temp; 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
     } 
 Tcode=ivector(1,100);    for (j=1;j<=n;j++) { 
    nbcode=imatrix(1,nvar,1,8);        for (i=1;i<j;i++) { 
    ncodemax[1]=1;        sum=a[i][j]; 
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
          a[i][j]=sum; 
    codtab=imatrix(1,100,1,10);      } 
    h=0;      big=0.0; 
    m=pow(2,cptcovn);      for (i=j;i<=n;i++) { 
          sum=a[i][j]; 
    for(k=1;k<=cptcovn; k++){        for (k=1;k<j;k++) 
      for(i=1; i <=(m/pow(2,k));i++){          sum -= a[i][k]*a[k][j]; 
        for(j=1; j <= ncodemax[k]; j++){        a[i][j]=sum; 
          for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){        if ( (dum=vv[i]*fabs(sum)) >= big) { 
            h++;          big=dum; 
            if (h>m) h=1;codtab[h][k]=j;          imax=i; 
          }        } 
        }      } 
      }      if (j != imax) { 
    }        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
    /*for(i=1; i <=m ;i++){          a[imax][k]=a[j][k]; 
      for(k=1; k <=cptcovn; k++){          a[j][k]=dum; 
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);        } 
      }        *d = -(*d); 
      printf("\n");        vv[imax]=vv[j]; 
    }      } 
   scanf("%d",i);*/      indx[j]=imax; 
          if (a[j][j] == 0.0) a[j][j]=TINY; 
    /* Calculates basic frequencies. Computes observed prevalence at single age      if (j != n) { 
        and prints on file fileres'p'. */        dum=1.0/(a[j][j]); 
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       } 
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    } 
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_vector(vv,1,n);  /* Doesn't work */
     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 */  
      void lubksb(double **a, int n, int *indx, double b[]) 
     /* 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] */    int i,ii=0,ip,j; 
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    double sum; 
     /*scanf("%d",i);*/   
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
          sum=b[ip]; 
     /*--------- results files --------------*/      b[ip]=b[i]; 
     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);      if (ii) 
            for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
    jk=1;      else if (sum) ii=i; 
    fprintf(ficres,"# Parameters\n");      b[i]=sum; 
    printf("# Parameters\n");    } 
    for(i=1,jk=1; i <=nlstate; i++){    for (i=n;i>=1;i--) { 
      for(k=1; k <=(nlstate+ndeath); k++){      sum=b[i]; 
        if (k != i)      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
          {      b[i]=sum/a[i][i]; 
            printf("%d%d ",i,k);    } 
            fprintf(ficres,"%1d%1d ",i,k);  } 
            for(j=1; j <=ncovmodel; j++){  
              printf("%f ",p[jk]);  void pstamp(FILE *fichier)
              fprintf(ficres,"%f ",p[jk]);  {
              jk++;    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
            }  }
            printf("\n");  
            fprintf(ficres,"\n");  /************ Frequencies ********************/
          }  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
      }  {  /* Some frequencies */
    }    
     int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     /* Computing hessian and covariance matrix */    int first;
     ftolhess=ftol; /* Usually correct */    double ***freq; /* Frequencies */
     hesscov(matcov, p, npar, delti, ftolhess, func);    double *pp, **prop;
     fprintf(ficres,"# Scales\n");    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     printf("# Scales\n");    char fileresp[FILENAMELENGTH];
      for(i=1,jk=1; i <=nlstate; i++){    
       for(j=1; j <=nlstate+ndeath; j++){    pp=vector(1,nlstate);
         if (j!=i) {    prop=matrix(1,nlstate,iagemin,iagemax+3);
           fprintf(ficres,"%1d%1d",i,j);    strcpy(fileresp,"p");
           printf("%1d%1d",i,j);    strcat(fileresp,fileres);
           for(k=1; k<=ncovmodel;k++){    if((ficresp=fopen(fileresp,"w"))==NULL) {
             printf(" %.5e",delti[jk]);      printf("Problem with prevalence resultfile: %s\n", fileresp);
             fprintf(ficres," %.5e",delti[jk]);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
             jk++;      exit(0);
           }    }
           printf("\n");    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
           fprintf(ficres,"\n");    j1=0;
         }    
       }    j=cptcoveff;
       }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      
     k=1;    first=1;
     fprintf(ficres,"# Covariance\n");  
     printf("# Covariance\n");    for(k1=1; k1<=j;k1++){
     for(i=1;i<=npar;i++){      for(i1=1; i1<=ncodemax[k1];i1++){
       /*  if (k>nlstate) k=1;        j1++;
       i1=(i-1)/(ncovmodel*nlstate)+1;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          scanf("%d", i);*/
       printf("%s%d%d",alph[k],i1,tab[i]);*/        for (i=-5; i<=nlstate+ndeath; i++)  
       fprintf(ficres,"%3d",i);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
       printf("%3d",i);            for(m=iagemin; m <= iagemax+3; m++)
       for(j=1; j<=i;j++){              freq[i][jk][m]=0;
         fprintf(ficres," %.5e",matcov[i][j]);  
         printf(" %.5e",matcov[i][j]);      for (i=1; i<=nlstate; i++)  
       }        for(m=iagemin; m <= iagemax+3; m++)
       fprintf(ficres,"\n");          prop[i][m]=0;
       printf("\n");        
       k++;        dateintsum=0;
     }        k2cpt=0;
            for (i=1; i<=imx; i++) {
     while((c=getc(ficpar))=='#' && c!= EOF){          bool=1;
       ungetc(c,ficpar);          if  (cptcovn>0) {
       fgets(line, MAXLINE, ficpar);            for (z1=1; z1<=cptcoveff; z1++) 
       puts(line);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       fputs(line,ficparo);                bool=0;
     }          }
     ungetc(c,ficpar);          if (bool==1){
              for(m=firstpass; m<=lastpass; m++){
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);              k2=anint[m][i]+(mint[m][i]/12.);
                  /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     if (fage <= 2) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       bage = agemin;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       fage = agemax;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     }                if (m<lastpass) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                }
 /*------------ gnuplot -------------*/                
 chdir(pathcd);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   if((ficgp=fopen("graph.plt","w"))==NULL) {                  dateintsum=dateintsum+k2;
     printf("Problem with file graph.gp");goto end;                  k2cpt++;
   }                }
 #ifdef windows                /*}*/
   fprintf(ficgp,"cd \"%s\" \n",pathc);            }
 #endif          }
 m=pow(2,cptcovn);        }
           
  /* 1eme*/        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   for (cpt=1; cpt<= nlstate ; cpt ++) {        pstamp(ficresp);
    for (k1=1; k1<= m ; k1 ++) {        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
 #ifdef windows          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     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);          fprintf(ficresp, "**********\n#");
 #endif        }
 #ifdef unix        for(i=1; i<=nlstate;i++) 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 #endif        fprintf(ficresp, "\n");
         
 for (i=1; i<= nlstate ; i ++) {        for(i=iagemin; i <= iagemax+3; i++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          if(i==iagemax+3){
   else fprintf(ficgp," \%%*lf (\%%*lf)");            fprintf(ficlog,"Total");
 }          }else{
     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(first==1){
     for (i=1; i<= nlstate ; i ++) {              first=0;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              printf("See log file for details...\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");            }
 }            fprintf(ficlog,"Age %d", i);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          }
      for (i=1; i<= nlstate ; i ++) {          for(jk=1; jk <=nlstate ; jk++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");              pp[jk] += freq[jk][m][i]; 
 }            }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          for(jk=1; jk <=nlstate ; jk++){
 #ifdef unix            for(m=-1, pos=0; m <=0 ; m++)
 fprintf(ficgp,"\nset ter gif small size 400,300");              pos += freq[jk][m][i];
 #endif            if(pp[jk]>=1.e-10){
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              if(first==1){
    }              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   }              }
   /*2 eme*/              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
   for (k1=1; k1<= m ; k1 ++) {              if(first==1)
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                  fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     for (i=1; i<= nlstate+1 ; i ++) {            }
       k=2*i;          }
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {          for(jk=1; jk <=nlstate ; jk++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");              pp[jk] += freq[jk][m][i];
 }            }       
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);            pos += pp[jk];
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);            posprop += prop[jk][i];
       for (j=1; j<= nlstate+1 ; j ++) {          }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          for(jk=1; jk <=nlstate ; jk++){
         else fprintf(ficgp," \%%*lf (\%%*lf)");            if(pos>=1.e-5){
 }                if(first==1)
       fprintf(ficgp,"\" t\"\" w l 0,");                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*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== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");            }
       else fprintf(ficgp,"\" t\"\" w l 0,");            if( i <= iagemax){
     }              if(pos>=1.e-5){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   }                /*probs[i][jk][j1]= pp[jk]/pos;*/
                  /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   /*3eme*/              }
               else
   for (k1=1; k1<= m ; k1 ++) {                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     for (cpt=1; cpt<= nlstate ; cpt ++) {            }
       k=2+nlstate*(cpt-1);          }
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);          
       for (i=1; i< nlstate ; i ++) {          for(jk=-1; jk <=nlstate+ndeath; jk++)
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);            for(m=-1; m <=nlstate+ndeath; m++)
       }              if(freq[jk][m][i] !=0 ) {
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              if(first==1)
     }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                }
   /* CV preval stat */          if(i <= iagemax)
   for (k1=1; k1<= m ; k1 ++) {            fprintf(ficresp,"\n");
     for (cpt=1; cpt<nlstate ; cpt ++) {          if(first==1)
       k=3;            printf("Others in log...\n");
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);          fprintf(ficlog,"\n");
       for (i=1; i< nlstate ; i ++)        }
         fprintf(ficgp,"+$%d",k+i+1);      }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    }
          dateintmean=dateintsum/k2cpt; 
       l=3+(nlstate+ndeath)*cpt;   
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    fclose(ficresp);
       for (i=1; i< nlstate ; i ++) {    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
         l=3+(nlstate+ndeath)*cpt;    free_vector(pp,1,nlstate);
         fprintf(ficgp,"+$%d",l+i+1);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       }    /* End of Freq */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    }
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }  /************ Prevalence ********************/
   }  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   {  
   /* proba elementaires */    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   for(i=1,jk=1; i <=nlstate; i++){       in each health status at the date of interview (if between dateprev1 and dateprev2).
     for(k=1; k <=(nlstate+ndeath); k++){       We still use firstpass and lastpass as another selection.
       if (k != i) {    */
         /*  fprintf(ficgp,"%1d%1d ",i,k);*/   
         for(j=1; j <=ncovmodel; j++){    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
           fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);    double ***freq; /* Frequencies */
           jk++;    double *pp, **prop;
           fprintf(ficgp,"\n");    double pos,posprop; 
         }    double  y2; /* in fractional years */
       }    int iagemin, iagemax;
     }  
   }    iagemin= (int) agemin;
   for(jk=1; jk <=m; jk++) {    iagemax= (int) agemax;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    /*pp=vector(1,nlstate);*/
   for(i=1; i <=nlstate; i++) {    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     for(k=1; k <=(nlstate+ndeath); k++){    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       if (k != i) {    j1=0;
         fprintf(ficgp," exp(a%d%d+b%d%d*x",i,k,i,k);    
         for(j=3; j <=ncovmodel; j++)    j=cptcoveff;
           fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         fprintf(ficgp,")/(1");    
         for(k1=1; k1 <=(nlstate+ndeath); k1++)    for(k1=1; k1<=j;k1++){
           if (k1 != i) {      for(i1=1; i1<=ncodemax[k1];i1++){
             fprintf(ficgp,"+exp(a%d%d+b%d%d*x",i,k1,i,k1);        j1++;
             for(j=3; j <=ncovmodel; j++)        
               fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        for (i=1; i<=nlstate; i++)  
             fprintf(ficgp,")");          for(m=iagemin; m <= iagemax+3; m++)
           }            prop[i][m]=0.0;
         fprintf(ficgp,") t \"p%d%d\" ", i,k);       
       if ((i+k)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        for (i=1; i<=imx; i++) { /* Each individual */
       }          bool=1;
     }          if  (cptcovn>0) {
   }            for (z1=1; z1<=cptcoveff; z1++) 
 fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   }                bool=0;
   fclose(ficgp);          } 
              if (bool==1) { 
 chdir(path);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     free_matrix(agev,1,maxwav,1,imx);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     free_ivector(wav,1,imx);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                    if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
     free_imatrix(s,1,maxwav+1,1,n);                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];
     free_ivector(num,1,n);                  prop[s[m][i]][iagemax+3] += weight[i]; 
     free_vector(agedc,1,n);                } 
     free_vector(weight,1,n);              }
     /*free_matrix(covar,1,NCOVMAX,1,n);*/            } /* end selection of waves */
     fclose(ficparo);          }
     fclose(ficres);        }
    }        for(i=iagemin; i <= iagemax+3; i++){  
              
    /*________fin mle=1_________*/          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                posprop += prop[jk][i]; 
           } 
    
     /* No more information from the sample is required now */          for(jk=1; jk <=nlstate ; jk++){     
   /* Reads comments: lines beginning with '#' */            if( i <=  iagemax){ 
   while((c=getc(ficpar))=='#' && c!= EOF){              if(posprop>=1.e-5){ 
     ungetc(c,ficpar);                probs[i][jk][j1]= prop[jk][i]/posprop;
     fgets(line, MAXLINE, ficpar);              } 
     puts(line);            } 
     fputs(line,ficparo);          }/* end jk */ 
   }        }/* end i */ 
   ungetc(c,ficpar);      } /* end i1 */
      } /* end k1 */
   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);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    /*free_vector(pp,1,nlstate);*/
 /*--------- index.htm --------*/    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
   if((fichtm=fopen("index.htm","w"))==NULL)    {  
     printf("Problem with index.htm \n");goto end;  /************* Waves Concatenation ***************/
   }  
   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)
  fprintf(fichtm,"<body><ul> Imach, Version 0.63<hr> <li>Outputs files<br><br>\n  {
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>       Death is a valid wave (if date is known).
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>       and mw[mi+1][i]. dh depends on stepm.
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>       */
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>  
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    int i, mi, 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);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
  fprintf(fichtm," <li>Graphs</li>\n<p>");    int first;
     int j, k=0,jk, ju, jl;
  m=cptcovn;    double sum=0.;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    first=0;
     jmin=1e+5;
  j1=0;    jmax=-1;
  for(k1=1; k1<=m;k1++){    jmean=0.;
    for(i1=1; i1<=ncodemax[k1];i1++){    for(i=1; i<=imx; i++){
        j1++;      mi=0;
        if (cptcovn > 0) {      m=firstpass;
          fprintf(fichtm,"<hr>************ Results for covariates");      while(s[m][i] <= nlstate){
          for (cpt=1; cpt<=cptcovn;cpt++)        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);          mw[++mi][i]=m;
          fprintf(fichtm," ************\n<hr>");        if(m >=lastpass)
        }          break;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>        else
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              m++;
        for(cpt=1; cpt<nlstate;cpt++){      }/* end while */
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      if (s[m][i] > nlstate){
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        mi++;     /* Death is another wave */
        }        /* if(mi==0)  never been interviewed correctly before death */
     for(cpt=1; cpt<=nlstate;cpt++) {           /* Only death is a correct wave */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        mw[mi][i]=m;
 interval) in state (%d): v%s%d%d.gif <br>      }
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    
      }      wav[i]=mi;
      for(cpt=1; cpt<=nlstate;cpt++) {      if(mi==0){
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        nbwarn++;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        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,"\n<br>- Total life expectancy by age and          first=1;
 health expectancies in states (1) and (2): e%s%d.gif<br>        }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        if(first==1){
 fprintf(fichtm,"\n</body>");          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
    }        }
  }      } /* end mi==0 */
 fclose(fichtm);    } /* End individuals */
   
   /*--------------- Prevalence limit --------------*/    for(i=1; i<=imx; i++){
        for(mi=1; mi<wav[i];mi++){
   strcpy(filerespl,"pl");        if (stepm <=0)
   strcat(filerespl,fileres);          dh[mi][i]=1;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        else{
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   }            if (agedc[i] < 2*AGESUP) {
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   fprintf(ficrespl,"#Prevalence limit\n");              if(j==0) j=1;  /* Survives at least one month after exam */
   fprintf(ficrespl,"#Age ");              else if(j<0){
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);                nberr++;
   fprintf(ficrespl,"\n");                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 */
   prlim=matrix(1,nlstate,1,nlstate);                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);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                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]);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                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);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              }
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              k=k+1;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              if (j >= jmax){
   k=0;                jmax=j;
   agebase=agemin;                ijmax=i;
   agelim=agemax;              }
   ftolpl=1.e-10;              if (j <= jmin){
   i1=cptcovn;                jmin=j;
   if (cptcovn < 1){i1=1;}                ijmin=i;
               }
   for(cptcov=1;cptcov<=i1;cptcov++){              sum=sum+j;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         k=k+1;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/            }
         fprintf(ficrespl,"\n#****** ");          }
         for(j=1;j<=cptcovn;j++)          else{
           fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         fprintf(ficrespl,"******\n");  /*        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]); */
          
         for (age=agebase; age<=agelim; age++){            k=k+1;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            if (j >= jmax) {
           fprintf(ficrespl,"%.0f",age );              jmax=j;
           for(i=1; i<=nlstate;i++)              ijmax=i;
           fprintf(ficrespl," %.5f", prlim[i][i]);            }
           fprintf(ficrespl,"\n");            else if (j <= jmin){
         }              jmin=j;
       }              ijmin=i;
     }            }
   fclose(ficrespl);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   /*------------- h Pij x at various ages ------------*/            /*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]);*/
              if(j<0){
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);              nberr++;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {              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]);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   }            }
   printf("Computing pij: result on file '%s' \n", filerespij);            sum=sum+j;
            }
   stepsize=(int) (stepm+YEARM-1)/YEARM;          jk= j/stepm;
   if (stepm<=24) stepsize=2;          jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
   agelim=AGESUP;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   hstepm=stepsize*YEARM; /* Every year of age */            if(jl==0){
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */              dh[mi][i]=jk;
                bh[mi][i]=0;
   k=0;            }else{ /* We want a negative bias in order to only have interpolation ie
   for(cptcov=1;cptcov<=i1;cptcov++){                    * at the price of an extra matrix product in likelihood */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              dh[mi][i]=jk+1;
       k=k+1;              bh[mi][i]=ju;
         fprintf(ficrespij,"\n#****** ");            }
         for(j=1;j<=cptcovn;j++)          }else{
           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);            if(jl <= -ju){
         fprintf(ficrespij,"******\n");              dh[mi][i]=jk;
                      bh[mi][i]=jl;       /* bias is positive if real duration
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                                   * is higher than the multiple of stepm and negative otherwise.
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                                   */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            else{
           oldm=oldms;savm=savms;              dh[mi][i]=jk+1;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                bh[mi][i]=ju;
           fprintf(ficrespij,"# Age");            }
           for(i=1; i<=nlstate;i++)            if(dh[mi][i]==0){
             for(j=1; j<=nlstate+ndeath;j++)              dh[mi][i]=1; /* At least one step */
               fprintf(ficrespij," %1d-%1d",i,j);              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 (h=0; h<=nhstepm; h++){            }
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          } /* end if mle */
             for(i=1; i<=nlstate;i++)        }
               for(j=1; j<=nlstate+ndeath;j++)      } /* end wave */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    }
             fprintf(ficrespij,"\n");    jmean=sum/k;
           }    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);
           free_ma3x(p3mat,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);
           fprintf(ficrespij,"\n");   }
         }  
     }  /*********** Tricode ****************************/
   }  void tricode(int *Tvar, int **nbcode, int imx)
   {
   fclose(ficrespij);    
     int Ndum[20],ij=1, k, j, i, maxncov=19;
   /*---------- Health expectancies and variances ------------*/    int cptcode=0;
     cptcoveff=0; 
   strcpy(filerest,"t");   
   strcat(filerest,fileres);    for (k=0; k<maxncov; k++) Ndum[k]=0;
   if((ficrest=fopen(filerest,"w"))==NULL) {    for (k=1; k<=7; k++) ncodemax[k]=0;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
   }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
         ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   strcpy(filerese,"e");        Ndum[ij]++; /*store the modality */
   strcat(filerese,fileres);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   if((ficreseij=fopen(filerese,"w"))==NULL) {        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                                         Tvar[j]. If V=sex and male is 0 and 
   }                                         female is 1, then  cptcode=1.*/
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      }
   
  strcpy(fileresv,"v");      for (i=0; i<=cptcode; i++) {
   strcat(fileresv,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((ficresvij=fopen(fileresv,"w"))==NULL) {      }
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }      ij=1; 
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      for (i=1; i<=ncodemax[j]; i++) {
         for (k=0; k<= maxncov; k++) {
   k=0;          if (Ndum[k] != 0) {
   for(cptcov=1;cptcov<=i1;cptcov++){            nbcode[Tvar[j]][ij]=k; 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            /* 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; */
       k=k+1;            
       fprintf(ficrest,"\n#****** ");            ij++;
       for(j=1;j<=cptcovn;j++)          }
         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);          if (ij > ncodemax[j]) break; 
       fprintf(ficrest,"******\n");        }  
       } 
       fprintf(ficreseij,"\n#****** ");    }  
       for(j=1;j<=cptcovn;j++)  
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);   for (k=0; k< maxncov; k++) Ndum[k]=0;
       fprintf(ficreseij,"******\n");  
    for (i=1; i<=ncovmodel-2; i++) { 
       fprintf(ficresvij,"\n#****** ");     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
       for(j=1;j<=cptcovn;j++)     ij=Tvar[i];
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);     Ndum[ij]++;
       fprintf(ficresvij,"******\n");   }
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);   ij=1;
       oldm=oldms;savm=savms;   for (i=1; i<= maxncov; i++) {
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);       if((Ndum[i]!=0) && (i<=ncovcol)){
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);       Tvaraff[ij]=i; /*For printing */
       oldm=oldms;savm=savms;       ij++;
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);     }
         }
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");   
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);   cptcoveff=ij-1; /*Number of simple covariates*/
       fprintf(ficrest,"\n");  }
          
       hf=1;  /*********** Health Expectancies ****************/
       if (stepm >= YEARM) hf=stepm/YEARM;  
       epj=vector(1,nlstate+1);  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[] )
       for(age=bage; age <=fage ;age++){  
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  {
         fprintf(ficrest," %.0f",age);    /* Health expectancies, no variances */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    double age, agelim, hf;
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    double ***p3mat;
           }    double eip;
           epj[nlstate+1] +=epj[j];  
         }    pstamp(ficreseij);
         for(i=1, vepp=0.;i <=nlstate;i++)    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
           for(j=1;j <=nlstate;j++)    fprintf(ficreseij,"# Age");
             vepp += vareij[i][j][(int)age];    for(i=1; i<=nlstate;i++){
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));      for(j=1; j<=nlstate;j++){
         for(j=1;j <=nlstate;j++){        fprintf(ficreseij," e%1d%1d ",i,j);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));      }
         }      fprintf(ficreseij," e%1d. ",i);
         fprintf(ficrest,"\n");    }
       }    fprintf(ficreseij,"\n");
     }  
   }    
            if(estepm < stepm){
  fclose(ficreseij);      printf ("Problem %d lower than %d\n",estepm, stepm);
  fclose(ficresvij);    }
   fclose(ficrest);    else  hstepm=estepm;   
   fclose(ficpar);    /* We compute the life expectancy from trapezoids spaced every estepm months
   free_vector(epj,1,nlstate+1);     * This is mainly to measure the difference between two models: for example
   /*  scanf("%d ",i); */     * 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 
   /*------- Variance limit prevalence------*/       * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
 strcpy(fileresvpl,"vpl");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   strcat(fileresvpl,fileres);     * to compare the new estimate of Life expectancy with the same linear 
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {     * hypothesis. A more precise result, taking into account a more precise
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);     * curvature will be obtained if estepm is as small as stepm. */
     exit(0);  
   }    /* For example we decided to compute the life expectancy with the smallest unit */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    /* 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 
  k=0;       nstepm is the number of stepm from age to agelin. 
  for(cptcov=1;cptcov<=i1;cptcov++){       Look at hpijx to understand the reason of that which relies in memory size
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       and note for a fixed period like estepm months */
      k=k+1;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
      fprintf(ficresvpl,"\n#****** ");       survival function given by stepm (the optimization length). Unfortunately it
      for(j=1;j<=cptcovn;j++)       means that if the survival funtion is printed only each two years of age and if
        fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
      fprintf(ficresvpl,"******\n");       results. So we changed our mind and took the option of the best precision.
          */
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      oldm=oldms;savm=savms;  
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    agelim=AGESUP;
    }    /* nhstepm age range expressed in number of stepm */
  }    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   fclose(ficresvpl);    /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   /*---------- End : free ----------------*/    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
        
        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   free_matrix(matcov,1,npar,1,npar);      
   free_vector(delti,1,npar);      /* Computing expectancies */
        for(i=1; i<=nlstate;i++)
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   printf("End of Imach\n");            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */            
              /* 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]);*/
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/  
   /*printf("Total time was %d uSec.\n", total_usecs);*/          }
   /*------ End -----------*/  
       fprintf(ficreseij,"%3.0f",age );
  end:      for(i=1; i<=nlstate;i++){
 #ifdef windows        eip=0;
  chdir(pathcd);        for(j=1; j<=nlstate;j++){
 #endif          eip +=eij[i][j][(int)age];
  system("wgnuplot ../gp37mgw/graph.plt");          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
 #ifdef windows        fprintf(ficreseij,"%9.4f", eip );
   while (z[0] != 'q') {      }
     chdir(pathcd);      fprintf(ficreseij,"\n");
     printf("\nType e to edit output files, c to start again, and q for exiting: ");      
     scanf("%s",z);    }
     if (z[0] == 'c') system("./imach");    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     else if (z[0] == 'e') {    printf("\n");
       chdir(path);    fprintf(ficlog,"\n");
       system("index.htm");    
     }  }
     else if (z[0] == 'q') exit(0);  
   }  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  
 }  {
     /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .
     */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     double age, agelim, hf;
     double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
     double *xp, *xm;
     double **gp, **gm;
     double ***gradg, ***trgradg;
     int theta;
   
     double eip, vip;
   
     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 . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char  *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       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.1.121


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