Diff for /imach/src/imach.c between versions 1.3 and 1.108

version 1.3, 2001/05/02 17:21:42 version 1.108, 2006/01/19 18:05:42
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.108  2006/01/19 18:05:42  lievre
   individuals from different ages are interviewed on their health status    Gnuplot problem appeared...
   or degree of  disability. At least a second wave of interviews    To be fixed
   ("longitudinal") should  measure each new individual health status.  
   Health expectancies are computed from the transistions observed between    Revision 1.107  2006/01/19 16:20:37  brouard
   waves and are computed for each degree of severity of disability (number    Test existence of gnuplot in imach path
   of life states). More degrees you consider, more time is necessary to  
   reach the Maximum Likelihood of the parameters involved in the model.    Revision 1.106  2006/01/19 13:24:36  brouard
   The simplest model is the multinomial logistic model where pij is    Some cleaning and links added in html output
   the probabibility to be observed in state j at the second wave conditional  
   to be observed in state i at the first wave. Therefore the model is:    Revision 1.105  2006/01/05 20:23:19  lievre
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    *** empty log message ***
   is a covariate. If you want to have a more complex model than "constant and  
   age", you should modify the program where the markup    Revision 1.104  2005/09/30 16:11:43  lievre
     *Covariates have to be included here again* invites you to do it.    (Module): sump fixed, loop imx fixed, and simplifications.
   More covariates you add, less is the speed of the convergence.    (Module): If the status is missing at the last wave but we know
     that the person is alive, then we can code his/her status as -2
   The advantage that this computer programme claims, comes from that if the    (instead of missing=-1 in earlier versions) and his/her
   delay between waves is not identical for each individual, or if some    contributions to the likelihood is 1 - Prob of dying from last
   individual missed an interview, the information is not rounded or lost, but    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   taken into account using an interpolation or extrapolation.    the healthy state at last known wave). Version is 0.98
   hPijx is the probability to be  
   observed in state i at age x+h conditional to the observed state i at age    Revision 1.103  2005/09/30 15:54:49  lievre
   x. The delay 'h' can be split into an exact number (nh*stepm) of    (Module): sump fixed, loop imx fixed, and simplifications.
   unobserved intermediate  states. This elementary transition (by month or  
   quarter trimester, semester or year) is model as a multinomial logistic.    Revision 1.102  2004/09/15 17:31:30  brouard
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    Add the possibility to read data file including tab characters.
   and the contribution of each individual to the likelihood is simply hPijx.  
     Revision 1.101  2004/09/15 10:38:38  brouard
   Also this programme outputs the covariance matrix of the parameters but also    Fix on curr_time
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.100  2004/07/12 18:29:06  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Add version for Mac OS X. Just define UNIX in Makefile
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.99  2004/06/05 08:57:40  brouard
   from the European Union.    *** empty log message ***
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.98  2004/05/16 15:05:56  brouard
   can be accessed at http://euroreves.ined.fr/imach .    New version 0.97 . First attempt to estimate force of mortality
   **********************************************************************/    directly from the data i.e. without the need of knowing the health
      state at each age, but using a Gompertz model: log u =a + b*age .
 #include <math.h>    This is the basic analysis of mortality and should be done before any
 #include <stdio.h>    other analysis, in order to test if the mortality estimated from the
 #include <stdlib.h>    cross-longitudinal survey is different from the mortality estimated
 #include <unistd.h>    from other sources like vital statistic data.
   
 #define MAXLINE 256    The same imach parameter file can be used but the option for mle should be -3.
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Agnès, who wrote this part of the code, tried to keep most of the
 #define windows    former routines in order to include the new code within the former code.
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    The output is very simple: only an estimate of the intercept and of
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    the slope with 95% confident intervals.
   
 #define NINTERVMAX 8    Current limitations:
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    A) Even if you enter covariates, i.e. with the
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define NCOVMAX 8 /* Maximum number of covariates */    B) There is no computation of Life Expectancy nor Life Table.
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.97  2004/02/20 13:25:42  lievre
 #define AGESUP 130    Version 0.96d. Population forecasting command line is (temporarily)
 #define AGEBASE 40    suppressed.
   
     Revision 1.96  2003/07/15 15:38:55  brouard
 int nvar;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 static int cptcov;    rewritten within the same printf. Workaround: many printfs.
 int cptcovn;  
 int npar=NPARMAX;    Revision 1.95  2003/07/08 07:54:34  brouard
 int nlstate=2; /* Number of live states */    * imach.c (Repository):
 int ndeath=1; /* Number of dead states */    (Repository): Using imachwizard code to output a more meaningful covariance
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    matrix (cov(a12,c31) instead of numbers.
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.94  2003/06/27 13:00:02  brouard
 int maxwav; /* Maxim number of waves */    Just cleaning
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.93  2003/06/25 16:33:55  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    (Module): On windows (cygwin) function asctime_r doesn't
 double **oldm, **newm, **savm; /* Working pointers to matrices */    exist so I changed back to asctime which exists.
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    (Module): Version 0.96b
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;  
 FILE *ficgp, *fichtm;    Revision 1.92  2003/06/25 16:30:45  brouard
 FILE *ficreseij;    (Module): On windows (cygwin) function asctime_r doesn't
   char filerese[FILENAMELENGTH];    exist so I changed back to asctime which exists.
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Revision 1.91  2003/06/25 15:30:29  brouard
  FILE  *ficresvpl;    * imach.c (Repository): Duplicated warning errors corrected.
   char fileresvpl[FILENAMELENGTH];    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
     concerning matrix of covariance. It has extension -cov.htm.
   
 #define NR_END 1    Revision 1.90  2003/06/24 12:34:15  brouard
 #define FREE_ARG char*    (Module): Some bugs corrected for windows. Also, when
 #define FTOL 1.0e-10    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 #define NRANSI  
 #define ITMAX 200    Revision 1.89  2003/06/24 12:30:52  brouard
     (Module): Some bugs corrected for windows. Also, when
 #define TOL 2.0e-4    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.88  2003/06/23 17:54:56  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    * 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.
   
 #define GOLD 1.618034    Revision 1.87  2003/06/18 12:26:01  brouard
 #define GLIMIT 100.0    Version 0.96
 #define TINY 1.0e-20  
     Revision 1.86  2003/06/17 20:04:08  brouard
 static double maxarg1,maxarg2;    (Module): Change position of html and gnuplot routines and added
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    routine fileappend.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.85  2003/06/17 13:12:43  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    * imach.c (Repository): Check when date of death was earlier that
 #define rint(a) floor(a+0.5)    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
 static double sqrarg;    was wrong (infinity). We still send an "Error" but patch by
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    assuming that the date of death was just one stepm after the
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    interview.
     (Repository): Because some people have very long ID (first column)
 int imx;    we changed int to long in num[] and we added a new lvector for
 int stepm;    memory allocation. But we also truncated to 8 characters (left
 /* Stepm, step in month: minimum step interpolation*/    truncation)
     (Repository): No more line truncation errors.
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax;    Revision 1.84  2003/06/13 21:44:43  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    * imach.c (Repository): Replace "freqsummary" at a correct
 double **pmmij;    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
 double *weight;    parcimony.
 int **s; /* Status */    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab;    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.82  2003/06/05 15:57:20  brouard
     Add log in  imach.c and  fullversion number is now printed.
   
 /******************************************/  */
   /*
 void replace(char *s, char*t)     Interpolated Markov Chain
 {  
   int i;    Short summary of the programme:
   int lg=20;    
   i=0;    This program computes Healthy Life Expectancies from
   lg=strlen(t);    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   for(i=0; i<= lg; i++) {    first survey ("cross") where individuals from different ages are
     (s[i] = t[i]);    interviewed on their health status or degree of disability (in the
     if (t[i]== '\\') s[i]='/';    case of a health survey which is our main interest) -2- at least a
   }    second wave of interviews ("longitudinal") which measure each change
 }    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
 int nbocc(char *s, char occ)    model. More health states you consider, more time is necessary to reach the
 {    Maximum Likelihood of the parameters involved in the model.  The
   int i,j=0;    simplest model is the multinomial logistic model where pij is the
   int lg=20;    probability to be observed in state j at the second wave
   i=0;    conditional to be observed in state i at the first wave. Therefore
   lg=strlen(s);    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   for(i=0; i<= lg; i++) {    'age' is age and 'sex' is a covariate. If you want to have a more
   if  (s[i] == occ ) j++;    complex model than "constant and age", you should modify the program
   }    where the markup *Covariates have to be included here again* invites
   return j;    you to do it.  More covariates you add, slower the
 }    convergence.
   
 void cutv(char *u,char *v, char*t, char occ)    The advantage of this computer programme, compared to a simple
 {    multinomial logistic model, is clear when the delay between waves is not
   int i,lg,j,p;    identical for each individual. Also, if a individual missed an
   i=0;    intermediate interview, the information is lost, but taken into
   for(j=0; j<=strlen(t)-1; j++) {    account using an interpolation or extrapolation.  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    hPijx is the probability to be observed in state i at age x+h
     conditional to the observed state i at age x. The delay 'h' can be
   lg=strlen(t);    split into an exact number (nh*stepm) of unobserved intermediate
   for(j=0; j<p; j++) {    states. This elementary transition (by month, quarter,
     (u[j] = t[j]);    semester or year) is modelled as a multinomial logistic.  The hPx
     u[p]='\0';    matrix is simply the matrix product of nh*stepm elementary matrices
   }    and the contribution of each individual to the likelihood is simply
     hPijx.
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    Also this programme outputs the covariance matrix of the parameters but also
   }    of the life expectancies. It also computes the stable prevalence. 
 }    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 /********************** nrerror ********************/             Institut national d'études démographiques, Paris.
     This software have been partly granted by Euro-REVES, a concerted action
 void nrerror(char error_text[])    from the European Union.
 {    It is copyrighted identically to a GNU software product, ie programme and
   fprintf(stderr,"ERREUR ...\n");    software can be distributed freely for non commercial use. Latest version
   fprintf(stderr,"%s\n",error_text);    can be accessed at http://euroreves.ined.fr/imach .
   exit(1);  
 }    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 /*********************** vector *******************/    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 double *vector(int nl, int nh)    
 {    **********************************************************************/
   double *v;  /*
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    main
   if (!v) nrerror("allocation failure in vector");    read parameterfile
   return v-nl+NR_END;    read datafile
 }    concatwav
     freqsummary
 /************************ free vector ******************/    if (mle >= 1)
 void free_vector(double*v, int nl, int nh)      mlikeli
 {    print results files
   free((FREE_ARG)(v+nl-NR_END));    if mle==1 
 }       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 /************************ivector *******************************/        begin-prev-date,...
 int *ivector(long nl,long nh)    open gnuplot file
 {    open html file
   int *v;    stable prevalence
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));     for age prevalim()
   if (!v) nrerror("allocation failure in ivector");    h Pij x
   return v-nl+NR_END;    variance of p varprob
 }    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
 /******************free ivector **************************/    Variance-covariance of DFLE
 void free_ivector(int *v, long nl, long nh)    prevalence()
 {     movingaverage()
   free((FREE_ARG)(v+nl-NR_END));    varevsij() 
 }    if popbased==1 varevsij(,popbased)
     total life expectancies
 /******************* imatrix *******************************/    Variance of stable prevalence
 int **imatrix(long nrl, long nrh, long ncl, long nch)   end
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  */
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;  
     
   /* allocate pointers to rows */  #include <math.h>
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #include <stdio.h>
   if (!m) nrerror("allocation failure 1 in matrix()");  #include <stdlib.h>
   m += NR_END;  #include <string.h>
   m -= nrl;  #include <unistd.h>
    
    #include <sys/types.h>
   /* allocate rows and set pointers to them */  #include <sys/stat.h>
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #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"
    
   /* return pointer to array of pointers to rows */  /* #include <libintl.h> */
   return m;  /* #define _(String) gettext (String) */
 }  
   #define MAXLINE 256
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)  #define GNUPLOTPROGRAM "gnuplot"
       int **m;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       long nch,ncl,nrh,nrl;  #define FILENAMELENGTH 132
      /* free an int matrix allocated by imatrix() */  
 {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   free((FREE_ARG) (m+nrl-NR_END));  
 }  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  #define NINTERVMAX 8
 {  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   double **m;  #define NCOVMAX 8 /* Maximum number of covariates */
   #define MAXN 20000
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define YEARM 12. /* Number of months per year */
   if (!m) nrerror("allocation failure 1 in matrix()");  #define AGESUP 130
   m += NR_END;  #define AGEBASE 40
   m -= nrl;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   #ifdef UNIX
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define DIRSEPARATOR '/'
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define CHARSEPARATOR "/"
   m[nrl] += NR_END;  #define ODIRSEPARATOR '\\'
   m[nrl] -= ncl;  #else
   #define DIRSEPARATOR '\\'
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define CHARSEPARATOR "\\"
   return m;  #define ODIRSEPARATOR '/'
 }  #endif
   
 /*************************free matrix ************************/  /* $Id$ */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  /* $State$ */
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
   free((FREE_ARG)(m+nrl-NR_END));  char fullversion[]="$Revision$ $Date$"; 
 }  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   int nvar;
 /******************* ma3x *******************************/  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  int npar=NPARMAX;
 {  int nlstate=2; /* Number of live states */
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  int ndeath=1; /* Number of dead states */
   double ***m;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  int *wav; /* Number of waves for this individuual 0 is possible */
   m += NR_END;  int maxwav; /* Maxim number of waves */
   m -= nrl;  int jmin, jmax; /* min, max spacing between 2 waves */
   int gipmx, gsw; /* Global variables on the number of contributions 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));                     to the likelihood and the sum of weights (done by funcone)*/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int mle, weightopt;
   m[nrl] += NR_END;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   m[nrl] -= ncl;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  double **oldm, **newm, **savm; /* Working pointers to matrices */
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   m[nrl][ncl] += NR_END;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   m[nrl][ncl] -= nll;  FILE *ficlog, *ficrespow;
   for (j=ncl+1; j<=nch; j++)  int globpr; /* Global variable for printing or not */
     m[nrl][j]=m[nrl][j-1]+nlay;  double fretone; /* Only one call to likelihood */
    long ipmx; /* Number of contributions */
   for (i=nrl+1; i<=nrh; i++) {  double sw; /* Sum of weights */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  char filerespow[FILENAMELENGTH];
     for (j=ncl+1; j<=nch; j++)  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       m[i][j]=m[i][j-1]+nlay;  FILE *ficresilk;
   }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   return m;  FILE *ficresprobmorprev;
 }  FILE *fichtm, *fichtmcov; /* Html File */
   FILE *ficreseij;
 /*************************free ma3x ************************/  char filerese[FILENAMELENGTH];
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  FILE  *ficresvij;
 {  char fileresv[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  FILE  *ficresvpl;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  char fileresvpl[FILENAMELENGTH];
   free((FREE_ARG)(m+nrl-NR_END));  char title[MAXLINE];
 }  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 /***************** f1dim *************************/  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 extern int ncom;  char command[FILENAMELENGTH];
 extern double *pcom,*xicom;  int  outcmd=0;
 extern double (*nrfunc)(double []);  
    char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 double f1dim(double x)  
 {  char filelog[FILENAMELENGTH]; /* Log file */
   int j;  char filerest[FILENAMELENGTH];
   double f;  char fileregp[FILENAMELENGTH];
   double *xt;  char popfile[FILENAMELENGTH];
    
   xt=vector(1,ncom);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   free_vector(xt,1,ncom);  struct timezone tzp;
   return f;  extern int gettimeofday();
 }  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   long time_value;
 /*****************brent *************************/  extern long time();
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  char strcurr[80], strfor[80];
 {  
   int iter;  #define NR_END 1
   double a,b,d,etemp;  #define FREE_ARG char*
   double fu,fv,fw,fx;  #define FTOL 1.0e-10
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;  #define NRANSI 
   double e=0.0;  #define ITMAX 200 
    
   a=(ax < cx ? ax : cx);  #define TOL 2.0e-4 
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;  #define CGOLD 0.3819660 
   fw=fv=fx=(*f)(x);  #define ZEPS 1.0e-10 
   for (iter=1;iter<=ITMAX;iter++) {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  #define GOLD 1.618034 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  #define GLIMIT 100.0 
     printf(".");fflush(stdout);  #define TINY 1.0e-20 
 #ifdef DEBUG  
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  static double maxarg1,maxarg2;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 #endif  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    
       *xmin=x;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       return fx;  #define rint(a) floor(a+0.5)
     }  
     ftemp=fu;  static double sqrarg;
     if (fabs(e) > tol1) {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       r=(x-w)*(fx-fv);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       q=(x-v)*(fx-fw);  int agegomp= AGEGOMP;
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);  int imx; 
       if (q > 0.0) p = -p;  int stepm=1;
       q=fabs(q);  /* Stepm, step in month: minimum step interpolation*/
       etemp=e;  
       e=d;  int estepm;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {  int m,nb;
         d=p/q;  long *num;
         u=x+d;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
         if (u-a < tol2 || b-u < tol2)  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
           d=SIGN(tol1,xm-x);  double **pmmij, ***probs;
       }  double *ageexmed,*agecens;
     } else {  double dateintmean=0;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  double *weight;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  int **s; /* Status */
     fu=(*f)(u);  double *agedc, **covar, idx;
     if (fu <= fx) {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       if (u >= x) a=x; else b=x;  double *lsurv, *lpop, *tpop;
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
         } else {  double ftolhess; /* Tolerance for computing hessian */
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  /**************** split *************************/
             v=w;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
             w=u;  {
             fv=fw;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
             fw=fu;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
           } else if (fu <= fv || v == x || v == w) {    */ 
             v=u;    char  *ss;                            /* pointer */
             fv=fu;    int   l1, l2;                         /* length counters */
           }  
         }    l1 = strlen(path );                   /* length of path */
   }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   nrerror("Too many iterations in brent");    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   *xmin=x;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   return fx;      strcpy( name, path );               /* we got the fullname name because no directory */
 }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 /****************** mnbrak ***********************/      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
             double (*func)(double))        return( GLOCK_ERROR_GETCWD );
 {      }
   double ulim,u,r,q, dum;      /* got dirc from getcwd*/
   double fu;      printf(" DIRC = %s \n",dirc);
      } else {                              /* strip direcotry from path */
   *fa=(*func)(*ax);      ss++;                               /* after this, the filename */
   *fb=(*func)(*bx);      l2 = strlen( ss );                  /* length of filename */
   if (*fb > *fa) {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     SHFT(dum,*ax,*bx,dum)      strcpy( name, ss );         /* save file name */
       SHFT(dum,*fb,*fa,dum)      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       }      dirc[l1-l2] = 0;                    /* add zero */
   *cx=(*bx)+GOLD*(*bx-*ax);      printf(" DIRC2 = %s \n",dirc);
   *fc=(*func)(*cx);    }
   while (*fb > *fc) {    /* We add a separator at the end of dirc if not exists */
     r=(*bx-*ax)*(*fb-*fc);    l1 = strlen( dirc );                  /* length of directory */
     q=(*bx-*cx)*(*fb-*fa);    if( dirc[l1-1] != DIRSEPARATOR ){
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      dirc[l1] =  DIRSEPARATOR;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));      dirc[l1+1] = 0; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);      printf(" DIRC3 = %s \n",dirc);
     if ((*bx-u)*(u-*cx) > 0.0) {    }
       fu=(*func)(u);    ss = strrchr( name, '.' );            /* find last / */
     } else if ((*cx-u)*(u-ulim) > 0.0) {    if (ss >0){
       fu=(*func)(u);      ss++;
       if (fu < *fc) {      strcpy(ext,ss);                     /* save extension */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      l1= strlen( name);
           SHFT(*fb,*fc,fu,(*func)(u))      l2= strlen(ss)+1;
           }      strncpy( finame, name, l1-l2);
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      finame[l1-l2]= 0;
       u=ulim;    }
       fu=(*func)(u);  
     } else {    return( 0 );                          /* we're done */
       u=(*cx)+GOLD*(*cx-*bx);  }
       fu=(*func)(u);  
     }  
     SHFT(*ax,*bx,*cx,u)  /******************************************/
       SHFT(*fa,*fb,*fc,fu)  
       }  void replace_back_to_slash(char *s, char*t)
 }  {
     int i;
 /*************** linmin ************************/    int lg=0;
     i=0;
 int ncom;    lg=strlen(t);
 double *pcom,*xicom;    for(i=0; i<= lg; i++) {
 double (*nrfunc)(double []);      (s[i] = t[i]);
        if (t[i]== '\\') s[i]='/';
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    }
 {  }
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);  int nbocc(char *s, char occ)
   double f1dim(double x);  {
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    int i,j=0;
               double *fc, double (*func)(double));    int lg=20;
   int j;    i=0;
   double xx,xmin,bx,ax;    lg=strlen(s);
   double fx,fb,fa;    for(i=0; i<= lg; i++) {
      if  (s[i] == occ ) j++;
   ncom=n;    }
   pcom=vector(1,n);    return j;
   xicom=vector(1,n);  }
   nrfunc=func;  
   for (j=1;j<=n;j++) {  void cutv(char *u,char *v, char*t, char occ)
     pcom[j]=p[j];  {
     xicom[j]=xi[j];    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
   }       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
   ax=0.0;       gives u="abcedf" and v="ghi2j" */
   xx=1.0;    int i,lg,j,p=0;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    i=0;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    for(j=0; j<=strlen(t)-1; j++) {
 #ifdef DEBUG      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    }
 #endif  
   for (j=1;j<=n;j++) {    lg=strlen(t);
     xi[j] *= xmin;    for(j=0; j<p; j++) {
     p[j] += xi[j];      (u[j] = t[j]);
   }    }
   free_vector(xicom,1,n);       u[p]='\0';
   free_vector(pcom,1,n);  
 }     for(j=0; j<= lg; j++) {
       if (j>=(p+1))(v[j-p-1] = t[j]);
 /*************** powell ************************/    }
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  }
             double (*func)(double []))  
 {  /********************** nrerror ********************/
   void linmin(double p[], double xi[], int n, double *fret,  
               double (*func)(double []));  void nrerror(char error_text[])
   int i,ibig,j;  {
   double del,t,*pt,*ptt,*xit;    fprintf(stderr,"ERREUR ...\n");
   double fp,fptt;    fprintf(stderr,"%s\n",error_text);
   double *xits;    exit(EXIT_FAILURE);
   pt=vector(1,n);  }
   ptt=vector(1,n);  /*********************** vector *******************/
   xit=vector(1,n);  double *vector(int nl, int nh)
   xits=vector(1,n);  {
   *fret=(*func)(p);    double *v;
   for (j=1;j<=n;j++) pt[j]=p[j];    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   for (*iter=1;;++(*iter)) {    if (!v) nrerror("allocation failure in vector");
     fp=(*fret);    return v-nl+NR_END;
     ibig=0;  }
     del=0.0;  
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  /************************ free vector ******************/
     for (i=1;i<=n;i++)  void free_vector(double*v, int nl, int nh)
       printf(" %d %.12f",i, p[i]);  {
     printf("\n");    free((FREE_ARG)(v+nl-NR_END));
     for (i=1;i<=n;i++) {  }
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  /************************ivector *******************************/
 #ifdef DEBUG  int *ivector(long nl,long nh)
       printf("fret=%lf \n",*fret);  {
 #endif    int *v;
       printf("%d",i);fflush(stdout);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       linmin(p,xit,n,fret,func);    if (!v) nrerror("allocation failure in ivector");
       if (fabs(fptt-(*fret)) > del) {    return v-nl+NR_END;
         del=fabs(fptt-(*fret));  }
         ibig=i;  
       }  /******************free ivector **************************/
 #ifdef DEBUG  void free_ivector(int *v, long nl, long nh)
       printf("%d %.12e",i,(*fret));  {
       for (j=1;j<=n;j++) {    free((FREE_ARG)(v+nl-NR_END));
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  }
         printf(" x(%d)=%.12e",j,xit[j]);  
       }  /************************lvector *******************************/
       for(j=1;j<=n;j++)  long *lvector(long nl,long nh)
         printf(" p=%.12e",p[j]);  {
       printf("\n");    long *v;
 #endif    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     }    if (!v) nrerror("allocation failure in ivector");
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    return v-nl+NR_END;
 #ifdef DEBUG  }
       int k[2],l;  
       k[0]=1;  /******************free lvector **************************/
       k[1]=-1;  void free_lvector(long *v, long nl, long nh)
       printf("Max: %.12e",(*func)(p));  {
       for (j=1;j<=n;j++)    free((FREE_ARG)(v+nl-NR_END));
         printf(" %.12e",p[j]);  }
       printf("\n");  
       for(l=0;l<=1;l++) {  /******************* imatrix *******************************/
         for (j=1;j<=n;j++) {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  { 
         }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    int **m; 
       }    
 #endif    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
       free_vector(xit,1,n);    m += NR_END; 
       free_vector(xits,1,n);    m -= nrl; 
       free_vector(ptt,1,n);    
       free_vector(pt,1,n);    
       return;    /* allocate rows and set pointers to them */ 
     }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     for (j=1;j<=n;j++) {    m[nrl] += NR_END; 
       ptt[j]=2.0*p[j]-pt[j];    m[nrl] -= ncl; 
       xit[j]=p[j]-pt[j];    
       pt[j]=p[j];    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     }    
     fptt=(*func)(ptt);    /* return pointer to array of pointers to rows */ 
     if (fptt < fp) {    return m; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  } 
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  /****************** free_imatrix *************************/
         for (j=1;j<=n;j++) {  void free_imatrix(m,nrl,nrh,ncl,nch)
           xi[j][ibig]=xi[j][n];        int **m;
           xi[j][n]=xit[j];        long nch,ncl,nrh,nrl; 
         }       /* free an int matrix allocated by imatrix() */ 
 #ifdef DEBUG  { 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         for(j=1;j<=n;j++)    free((FREE_ARG) (m+nrl-NR_END)); 
           printf(" %.12e",xit[j]);  } 
         printf("\n");  
 #endif  /******************* matrix *******************************/
       }  double **matrix(long nrl, long nrh, long ncl, long nch)
     }  {
   }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 }    double **m;
   
 /**** Prevalence limit ****************/    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    m += NR_END;
 {    m -= nrl;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  
      matrix by transitions matrix until convergence is reached */    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   int i, ii,j,k;    m[nrl] += NR_END;
   double min, max, maxmin, maxmax,sumnew=0.;    m[nrl] -= ncl;
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double **newm;    return m;
   double agefin, delaymax=50 ; /* Max number of years to converge */    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
      */
   for (ii=1;ii<=nlstate+ndeath;ii++)  }
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /*************************free matrix ************************/
     }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  {
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     newm=savm;    free((FREE_ARG)(m+nrl-NR_END));
     /* Covariates have to be included here again */  }
     cov[1]=1.;  
     cov[2]=agefin;  /******************* ma3x *******************************/
     if (cptcovn>0){  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       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]]);*/}  {
     }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    double ***m;
   
     savm=oldm;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     oldm=newm;    if (!m) nrerror("allocation failure 1 in matrix()");
     maxmax=0.;    m += NR_END;
     for(j=1;j<=nlstate;j++){    m -= nrl;
       min=1.;  
       max=0.;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       for(i=1; i<=nlstate; i++) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         sumnew=0;    m[nrl] += NR_END;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    m[nrl] -= ncl;
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         min=FMIN(min,prlim[i][j]);  
       }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       maxmin=max-min;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       maxmax=FMAX(maxmax,maxmin);    m[nrl][ncl] += NR_END;
     }    m[nrl][ncl] -= nll;
     if(maxmax < ftolpl){    for (j=ncl+1; j<=nch; j++) 
       return prlim;      m[nrl][j]=m[nrl][j-1]+nlay;
     }    
   }    for (i=nrl+1; i<=nrh; i++) {
 }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       for (j=ncl+1; j<=nch; j++) 
 /*************** transition probabilities **********/        m[i][j]=m[i][j-1]+nlay;
     }
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    return m; 
 {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   double s1, s2;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   /*double t34;*/    */
   int i,j,j1, nc, ii, jj;  }
   
     for(i=1; i<= nlstate; i++){  /*************************free ma3x ************************/
     for(j=1; j<i;j++){  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  {
         /*s2 += param[i][j][nc]*cov[nc];*/    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    free((FREE_ARG)(m+nrl-NR_END));
       }  }
       ps[i][j]=s2;  
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  /*************** function subdirf ***********/
     }  char *subdirf(char fileres[])
     for(j=i+1; j<=nlstate+ndeath;j++){  {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    /* Caution optionfilefiname is hidden */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    strcpy(tmpout,optionfilefiname);
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    strcat(tmpout,"/"); /* Add to the right */
       }    strcat(tmpout,fileres);
       ps[i][j]=s2;    return tmpout;
     }  }
   }  
   for(i=1; i<= nlstate; i++){  /*************** function subdirf2 ***********/
      s1=0;  char *subdirf2(char fileres[], char *preop)
     for(j=1; j<i; j++)  {
       s1+=exp(ps[i][j]);    
     for(j=i+1; j<=nlstate+ndeath; j++)    /* Caution optionfilefiname is hidden */
       s1+=exp(ps[i][j]);    strcpy(tmpout,optionfilefiname);
     ps[i][i]=1./(s1+1.);    strcat(tmpout,"/");
     for(j=1; j<i; j++)    strcat(tmpout,preop);
       ps[i][j]= exp(ps[i][j])*ps[i][i];    strcat(tmpout,fileres);
     for(j=i+1; j<=nlstate+ndeath; j++)    return tmpout;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  }
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  
   } /* end i */  /*************** function subdirf3 ***********/
   char *subdirf3(char fileres[], char *preop, char *preop2)
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  {
     for(jj=1; jj<= nlstate+ndeath; jj++){    
       ps[ii][jj]=0;    /* Caution optionfilefiname is hidden */
       ps[ii][ii]=1;    strcpy(tmpout,optionfilefiname);
     }    strcat(tmpout,"/");
   }    strcat(tmpout,preop);
     strcat(tmpout,preop2);
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    strcat(tmpout,fileres);
     for(jj=1; jj<= nlstate+ndeath; jj++){    return tmpout;
      printf("%lf ",ps[ii][jj]);  }
    }  
     printf("\n ");  /***************** f1dim *************************/
     }  extern int ncom; 
     printf("\n ");printf("%lf ",cov[2]);*/  extern double *pcom,*xicom;
 /*  extern double (*nrfunc)(double []); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);   
   goto end;*/  double f1dim(double x) 
     return ps;  { 
 }    int j; 
     double f;
 /**************** Product of 2 matrices ******************/    double *xt; 
    
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    xt=vector(1,ncom); 
 {    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    f=(*nrfunc)(xt); 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    free_vector(xt,1,ncom); 
   /* in, b, out are matrice of pointers which should have been initialized    return f; 
      before: only the contents of out is modified. The function returns  } 
      a pointer to pointers identical to out */  
   long i, j, k;  /*****************brent *************************/
   for(i=nrl; i<= nrh; i++)  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     for(k=ncolol; k<=ncoloh; k++)  { 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    int iter; 
         out[i][k] +=in[i][j]*b[j][k];    double a,b,d,etemp;
     double fu,fv,fw,fx;
   return out;    double ftemp;
 }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     double e=0.0; 
    
 /************* Higher Matrix Product ***************/    a=(ax < cx ? ax : cx); 
     b=(ax > cx ? ax : cx); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    x=w=v=bx; 
 {    fw=fv=fx=(*f)(x); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    for (iter=1;iter<=ITMAX;iter++) { 
      duration (i.e. until      xm=0.5*(a+b); 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
      (typically every 2 years instead of every month which is too big).      printf(".");fflush(stdout);
      Model is determined by parameters x and covariates have to be      fprintf(ficlog,".");fflush(ficlog);
      included manually here.  #ifdef DEBUG
       printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
      */      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)))) { */
   int i, j, d, h, k;  #endif
   double **out, cov[NCOVMAX];      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   double **newm;        *xmin=x; 
         return fx; 
   /* Hstepm could be zero and should return the unit matrix */      } 
   for (i=1;i<=nlstate+ndeath;i++)      ftemp=fu;
     for (j=1;j<=nlstate+ndeath;j++){      if (fabs(e) > tol1) { 
       oldm[i][j]=(i==j ? 1.0 : 0.0);        r=(x-w)*(fx-fv); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);        q=(x-v)*(fx-fw); 
     }        p=(x-v)*q-(x-w)*r; 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        q=2.0*(q-r); 
   for(h=1; h <=nhstepm; h++){        if (q > 0.0) p = -p; 
     for(d=1; d <=hstepm; d++){        q=fabs(q); 
       newm=savm;        etemp=e; 
       /* Covariates have to be included here again */        e=d; 
       cov[1]=1.;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       if (cptcovn>0){        else { 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];          d=p/q; 
     }          u=x+d; 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/          if (u-a < tol2 || b-u < tol2) 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/            d=SIGN(tol1,xm-x); 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        } 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      } else { 
       savm=oldm;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       oldm=newm;      } 
     }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     for(i=1; i<=nlstate+ndeath; i++)      fu=(*f)(u); 
       for(j=1;j<=nlstate+ndeath;j++) {      if (fu <= fx) { 
         po[i][j][h]=newm[i][j];        if (u >= x) a=x; else b=x; 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        SHFT(v,w,x,u) 
          */          SHFT(fv,fw,fx,fu) 
       }          } else { 
   } /* end h */            if (u < x) a=u; else b=u; 
   return po;            if (fu <= fw || w == x) { 
 }              v=w; 
               w=u; 
               fv=fw; 
 /*************** log-likelihood *************/              fw=fu; 
 double func( double *x)            } else if (fu <= fv || v == x || v == w) { 
 {              v=u; 
   int i, ii, j, k, mi, d;              fv=fu; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];            } 
   double **out;          } 
   double sw; /* Sum of weights */    } 
   double lli; /* Individual log likelihood */    nrerror("Too many iterations in brent"); 
   long ipmx;    *xmin=x; 
   /*extern weight */    return fx; 
   /* We are differentiating ll according to initial status */  } 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)  /****************** mnbrak ***********************/
 printf(" %d\n",s[4][i]);  
   */  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               double (*func)(double)) 
   for(k=1; k<=nlstate; k++) ll[k]=0.;  { 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    double ulim,u,r,q, dum;
        for(mi=1; mi<= wav[i]-1; mi++){    double fu; 
       for (ii=1;ii<=nlstate+ndeath;ii++)   
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    *fa=(*func)(*ax); 
             for(d=0; d<dh[mi][i]; d++){    *fb=(*func)(*bx); 
         newm=savm;    if (*fb > *fa) { 
           cov[1]=1.;      SHFT(dum,*ax,*bx,dum) 
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        SHFT(dum,*fb,*fa,dum) 
           if (cptcovn>0){        } 
             for (k=1; k<=cptcovn;k++) cov[2+k]=covar[1+k-1][i];    *cx=(*bx)+GOLD*(*bx-*ax); 
             }    *fc=(*func)(*cx); 
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    while (*fb > *fc) { 
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      r=(*bx-*ax)*(*fb-*fc); 
           savm=oldm;      q=(*bx-*cx)*(*fb-*fa); 
           oldm=newm;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
       } /* end mult */      if ((*bx-u)*(u-*cx) > 0.0) { 
            fu=(*func)(u); 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        fu=(*func)(u); 
       ipmx +=1;        if (fu < *fc) { 
       sw += weight[i];          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;            SHFT(*fb,*fc,fu,(*func)(u)) 
     } /* end of wave */            } 
   } /* end of individual */      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         u=ulim; 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        fu=(*func)(u); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      } else { 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        u=(*cx)+GOLD*(*cx-*bx); 
   return -l;        fu=(*func)(u); 
 }      } 
       SHFT(*ax,*bx,*cx,u) 
         SHFT(*fa,*fb,*fc,fu) 
 /*********** Maximum Likelihood Estimation ***************/        } 
   } 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  
 {  /*************** linmin ************************/
   int i,j, iter;  
   double **xi,*delti;  int ncom; 
   double fret;  double *pcom,*xicom;
   xi=matrix(1,npar,1,npar);  double (*nrfunc)(double []); 
   for (i=1;i<=npar;i++)   
     for (j=1;j<=npar;j++)  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       xi[i][j]=(i==j ? 1.0 : 0.0);  { 
   printf("Powell\n");    double brent(double ax, double bx, double cx, 
   powell(p,xi,npar,ftol,&iter,&fret,func);                 double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));                double *fc, double (*func)(double)); 
     int j; 
 }    double xx,xmin,bx,ax; 
     double fx,fb,fa;
 /**** Computes Hessian and covariance matrix ***/   
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    ncom=n; 
 {    pcom=vector(1,n); 
   double  **a,**y,*x,pd;    xicom=vector(1,n); 
   double **hess;    nrfunc=func; 
   int i, j,jk;    for (j=1;j<=n;j++) { 
   int *indx;      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
   double hessii(double p[], double delta, int theta, double delti[]);    } 
   double hessij(double p[], double delti[], int i, int j);    ax=0.0; 
   void lubksb(double **a, int npar, int *indx, double b[]) ;    xx=1.0; 
   void ludcmp(double **a, int npar, int *indx, double *d) ;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   #ifdef DEBUG
   hess=matrix(1,npar,1,npar);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   printf("\nCalculation of the hessian matrix. Wait...\n");  #endif
   for (i=1;i<=npar;i++){    for (j=1;j<=n;j++) { 
     printf("%d",i);fflush(stdout);      xi[j] *= xmin; 
     hess[i][i]=hessii(p,ftolhess,i,delti);      p[j] += xi[j]; 
     /*printf(" %f ",p[i]);*/    } 
   }    free_vector(xicom,1,n); 
     free_vector(pcom,1,n); 
   for (i=1;i<=npar;i++) {  } 
     for (j=1;j<=npar;j++)  {  
       if (j>i) {  char *asc_diff_time(long time_sec, char ascdiff[])
         printf(".%d%d",i,j);fflush(stdout);  {
         hess[i][j]=hessij(p,delti,i,j);    long sec_left, days, hours, minutes;
         hess[j][i]=hess[i][j];    days = (time_sec) / (60*60*24);
       }    sec_left = (time_sec) % (60*60*24);
     }    hours = (sec_left) / (60*60) ;
   }    sec_left = (sec_left) %(60*60);
   printf("\n");    minutes = (sec_left) /60;
     sec_left = (sec_left) % (60);
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
      return ascdiff;
   a=matrix(1,npar,1,npar);  }
   y=matrix(1,npar,1,npar);  
   x=vector(1,npar);  /*************** powell ************************/
   indx=ivector(1,npar);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   for (i=1;i<=npar;i++)              double (*func)(double [])) 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  { 
   ludcmp(a,npar,indx,&pd);    void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
   for (j=1;j<=npar;j++) {    int i,ibig,j; 
     for (i=1;i<=npar;i++) x[i]=0;    double del,t,*pt,*ptt,*xit;
     x[j]=1;    double fp,fptt;
     lubksb(a,npar,indx,x);    double *xits;
     for (i=1;i<=npar;i++){    int niterf, itmp;
       matcov[i][j]=x[i];  
     }    pt=vector(1,n); 
   }    ptt=vector(1,n); 
     xit=vector(1,n); 
   printf("\n#Hessian matrix#\n");    xits=vector(1,n); 
   for (i=1;i<=npar;i++) {    *fret=(*func)(p); 
     for (j=1;j<=npar;j++) {    for (j=1;j<=n;j++) pt[j]=p[j]; 
       printf("%.3e ",hess[i][j]);    for (*iter=1;;++(*iter)) { 
     }      fp=(*fret); 
     printf("\n");      ibig=0; 
   }      del=0.0; 
       last_time=curr_time;
   /* Recompute Inverse */      (void) gettimeofday(&curr_time,&tzp);
   for (i=1;i<=npar;i++)      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      /*    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);
   ludcmp(a,npar,indx,&pd);      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       */
   /*  printf("\n#Hessian matrix recomputed#\n");     for (i=1;i<=n;i++) {
         printf(" %d %.12f",i, p[i]);
   for (j=1;j<=npar;j++) {        fprintf(ficlog," %d %.12lf",i, p[i]);
     for (i=1;i<=npar;i++) x[i]=0;        fprintf(ficrespow," %.12lf", p[i]);
     x[j]=1;      }
     lubksb(a,npar,indx,x);      printf("\n");
     for (i=1;i<=npar;i++){      fprintf(ficlog,"\n");
       y[i][j]=x[i];      fprintf(ficrespow,"\n");fflush(ficrespow);
       printf("%.3e ",y[i][j]);      if(*iter <=3){
     }        tm = *localtime(&curr_time.tv_sec);
     printf("\n");        strcpy(strcurr,asctime(&tm));
   }  /*       asctime_r(&tm,strcurr); */
   */        forecast_time=curr_time; 
         itmp = strlen(strcurr);
   free_matrix(a,1,npar,1,npar);        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   free_matrix(y,1,npar,1,npar);          strcurr[itmp-1]='\0';
   free_vector(x,1,npar);        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   free_ivector(indx,1,npar);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   free_matrix(hess,1,npar,1,npar);        for(niterf=10;niterf<=30;niterf+=10){
           forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
           tmf = *localtime(&forecast_time.tv_sec);
 }  /*      asctime_r(&tmf,strfor); */
           strcpy(strfor,asctime(&tmf));
 /*************** hessian matrix ****************/          itmp = strlen(strfor);
 double hessii( double x[], double delta, int theta, double delti[])          if(strfor[itmp-1]=='\n')
 {          strfor[itmp-1]='\0';
   int i;          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);
   int l=1, lmax=20;          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);
   double k1,k2;        }
   double p2[NPARMAX+1];      }
   double res;      for (i=1;i<=n;i++) { 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   double fx;        fptt=(*fret); 
   int k=0,kmax=10;  #ifdef DEBUG
   double l1;        printf("fret=%lf \n",*fret);
         fprintf(ficlog,"fret=%lf \n",*fret);
   fx=func(x);  #endif
   for (i=1;i<=npar;i++) p2[i]=x[i];        printf("%d",i);fflush(stdout);
   for(l=0 ; l <=lmax; l++){        fprintf(ficlog,"%d",i);fflush(ficlog);
     l1=pow(10,l);        linmin(p,xit,n,fret,func); 
     delts=delt;        if (fabs(fptt-(*fret)) > del) { 
     for(k=1 ; k <kmax; k=k+1){          del=fabs(fptt-(*fret)); 
       delt = delta*(l1*k);          ibig=i; 
       p2[theta]=x[theta] +delt;        } 
       k1=func(p2)-fx;  #ifdef DEBUG
       p2[theta]=x[theta]-delt;        printf("%d %.12e",i,(*fret));
       k2=func(p2)-fx;        fprintf(ficlog,"%d %.12e",i,(*fret));
       /*res= (k1-2.0*fx+k2)/delt/delt; */        for (j=1;j<=n;j++) {
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
                printf(" x(%d)=%.12e",j,xit[j]);
 #ifdef DEBUG          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        }
 #endif        for(j=1;j<=n;j++) {
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          printf(" p=%.12e",p[j]);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          fprintf(ficlog," p=%.12e",p[j]);
         k=kmax;        }
       }        printf("\n");
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        fprintf(ficlog,"\n");
         k=kmax; l=lmax*10.;  #endif
       }      } 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         delts=delt;  #ifdef DEBUG
       }        int k[2],l;
     }        k[0]=1;
   }        k[1]=-1;
   delti[theta]=delts;        printf("Max: %.12e",(*func)(p));
   return res;        fprintf(ficlog,"Max: %.12e",(*func)(p));
          for (j=1;j<=n;j++) {
 }          printf(" %.12e",p[j]);
           fprintf(ficlog," %.12e",p[j]);
 double hessij( double x[], double delti[], int thetai,int thetaj)        }
 {        printf("\n");
   int i;        fprintf(ficlog,"\n");
   int l=1, l1, lmax=20;        for(l=0;l<=1;l++) {
   double k1,k2,k3,k4,res,fx;          for (j=1;j<=n;j++) {
   double p2[NPARMAX+1];            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   int k;            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]);
   fx=func(x);          }
   for (k=1; k<=2; k++) {          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for (i=1;i<=npar;i++) p2[i]=x[i];          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     p2[thetai]=x[thetai]+delti[thetai]/k;        }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  #endif
     k1=func(p2)-fx;  
    
     p2[thetai]=x[thetai]+delti[thetai]/k;        free_vector(xit,1,n); 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        free_vector(xits,1,n); 
     k2=func(p2)-fx;        free_vector(ptt,1,n); 
          free_vector(pt,1,n); 
     p2[thetai]=x[thetai]-delti[thetai]/k;        return; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      } 
     k3=func(p2)-fx;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
        for (j=1;j<=n;j++) { 
     p2[thetai]=x[thetai]-delti[thetai]/k;        ptt[j]=2.0*p[j]-pt[j]; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        xit[j]=p[j]-pt[j]; 
     k4=func(p2)-fx;        pt[j]=p[j]; 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      } 
 #ifdef DEBUG      fptt=(*func)(ptt); 
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);      if (fptt < fp) { 
 #endif        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   }        if (t < 0.0) { 
   return res;          linmin(p,xit,n,fret,func); 
 }          for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; 
 /************** Inverse of matrix **************/            xi[j][n]=xit[j]; 
 void ludcmp(double **a, int n, int *indx, double *d)          }
 {  #ifdef DEBUG
   int i,imax,j,k;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   double big,dum,sum,temp;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   double *vv;          for(j=1;j<=n;j++){
              printf(" %.12e",xit[j]);
   vv=vector(1,n);            fprintf(ficlog," %.12e",xit[j]);
   *d=1.0;          }
   for (i=1;i<=n;i++) {          printf("\n");
     big=0.0;          fprintf(ficlog,"\n");
     for (j=1;j<=n;j++)  #endif
       if ((temp=fabs(a[i][j])) > big) big=temp;        }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      } 
     vv[i]=1.0/big;    } 
   }  } 
   for (j=1;j<=n;j++) {  
     for (i=1;i<j;i++) {  /**** Prevalence limit (stable prevalence)  ****************/
       sum=a[i][j];  
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       a[i][j]=sum;  {
     }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     big=0.0;       matrix by transitions matrix until convergence is reached */
     for (i=j;i<=n;i++) {  
       sum=a[i][j];    int i, ii,j,k;
       for (k=1;k<j;k++)    double min, max, maxmin, maxmax,sumnew=0.;
         sum -= a[i][k]*a[k][j];    double **matprod2();
       a[i][j]=sum;    double **out, cov[NCOVMAX], **pmij();
       if ( (dum=vv[i]*fabs(sum)) >= big) {    double **newm;
         big=dum;    double agefin, delaymax=50 ; /* Max number of years to converge */
         imax=i;  
       }    for (ii=1;ii<=nlstate+ndeath;ii++)
     }      for (j=1;j<=nlstate+ndeath;j++){
     if (j != imax) {        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (k=1;k<=n;k++) {      }
         dum=a[imax][k];  
         a[imax][k]=a[j][k];     cov[1]=1.;
         a[j][k]=dum;   
       }   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       *d = -(*d);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       vv[imax]=vv[j];      newm=savm;
     }      /* Covariates have to be included here again */
     indx[j]=imax;       cov[2]=agefin;
     if (a[j][j] == 0.0) a[j][j]=TINY;    
     if (j != n) {        for (k=1; k<=cptcovn;k++) {
       dum=1.0/(a[j][j]);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          /*      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 (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   free_vector(vv,1,n);  /* Doesn't work */        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("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
 void lubksb(double **a, int n, int *indx, double b[])        /*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]);*/
   int i,ii=0,ip,j;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   double sum;  
        savm=oldm;
   for (i=1;i<=n;i++) {      oldm=newm;
     ip=indx[i];      maxmax=0.;
     sum=b[ip];      for(j=1;j<=nlstate;j++){
     b[ip]=b[i];        min=1.;
     if (ii)        max=0.;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        for(i=1; i<=nlstate; i++) {
     else if (sum) ii=i;          sumnew=0;
     b[i]=sum;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   }          prlim[i][j]= newm[i][j]/(1-sumnew);
   for (i=n;i>=1;i--) {          max=FMAX(max,prlim[i][j]);
     sum=b[i];          min=FMIN(min,prlim[i][j]);
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        }
     b[i]=sum/a[i][i];        maxmin=max-min;
   }        maxmax=FMAX(maxmax,maxmin);
 }      }
       if(maxmax < ftolpl){
 /************ Frequencies ********************/        return prlim;
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)      }
 {  /* Some frequencies */    }
    }
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */  /*************** transition probabilities ***************/ 
   double *pp;  
   double pos;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   FILE *ficresp;  {
   char fileresp[FILENAMELENGTH];    double s1, s2;
     /*double t34;*/
   pp=vector(1,nlstate);    int i,j,j1, nc, ii, jj;
   
   strcpy(fileresp,"p");      for(i=1; i<= nlstate; i++){
   strcat(fileresp,fileres);        for(j=1; j<i;j++){
   if((ficresp=fopen(fileresp,"w"))==NULL) {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     printf("Problem with prevalence resultfile: %s\n", fileresp);            /*s2 += param[i][j][nc]*cov[nc];*/
     exit(0);            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   }  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          }
   j1=0;          ps[i][j]=s2;
   /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   j=cptcovn;        }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        for(j=i+1; j<=nlstate+ndeath;j++){
           for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   for(k1=1; k1<=j;k1++){            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
    for(i1=1; i1<=ncodemax[k1];i1++){  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
        j1++;          }
           ps[i][j]=s2;
         for (i=-1; i<=nlstate+ndeath; i++)          }
          for (jk=-1; jk<=nlstate+ndeath; jk++)        }
            for(m=agemin; m <= agemax+3; m++)      /*ps[3][2]=1;*/
              freq[i][jk][m]=0;      
              for(i=1; i<= nlstate; i++){
        for (i=1; i<=imx; i++) {        s1=0;
          bool=1;        for(j=1; j<i; j++)
          if  (cptcovn>0) {          s1+=exp(ps[i][j]);
            for (z1=1; z1<=cptcovn; z1++)        for(j=i+1; j<=nlstate+ndeath; j++)
              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;          s1+=exp(ps[i][j]);
          }        ps[i][i]=1./(s1+1.);
           if (bool==1) {        for(j=1; j<i; j++)
            for(m=firstpass; m<=lastpass-1; m++){          ps[i][j]= exp(ps[i][j])*ps[i][i];
              if(agev[m][i]==0) agev[m][i]=agemax+1;        for(j=i+1; j<=nlstate+ndeath; j++)
              if(agev[m][i]==1) agev[m][i]=agemax+2;          ps[i][j]= exp(ps[i][j])*ps[i][i];
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      } /* end i */
            }      
          }      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
        }        for(jj=1; jj<= nlstate+ndeath; jj++){
         if  (cptcovn>0) {          ps[ii][jj]=0;
          fprintf(ficresp, "\n#Variable");          ps[ii][ii]=1;
          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);        }
        }      }
        fprintf(ficresp, "\n#");      
        for(i=1; i<=nlstate;i++)  
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
        fprintf(ficresp, "\n");  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
          /*         printf("ddd %lf ",ps[ii][jj]); */
   for(i=(int)agemin; i <= (int)agemax+3; i++){  /*       } */
     if(i==(int)agemax+3)  /*       printf("\n "); */
       printf("Total");  /*        } */
     else  /*        printf("\n ");printf("%lf ",cov[2]); */
       printf("Age %d", i);         /*
     for(jk=1; jk <=nlstate ; jk++){        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        goto end;*/
         pp[jk] += freq[jk][m][i];      return ps;
     }  }
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pos=0; m <=0 ; m++)  /**************** Product of 2 matrices ******************/
         pos += freq[jk][m][i];  
       if(pp[jk]>=1.e-10)  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  {
       else    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     }    /* in, b, out are matrice of pointers which should have been initialized 
     for(jk=1; jk <=nlstate ; jk++){       before: only the contents of out is modified. The function returns
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)       a pointer to pointers identical to out */
         pp[jk] += freq[jk][m][i];    long i, j, k;
     }    for(i=nrl; i<= nrh; i++)
     for(jk=1,pos=0; jk <=nlstate ; jk++)      for(k=ncolol; k<=ncoloh; k++)
       pos += pp[jk];        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     for(jk=1; jk <=nlstate ; jk++){          out[i][k] +=in[i][j]*b[j][k];
       if(pos>=1.e-5)  
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    return out;
       else  }
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  
       if( i <= (int) agemax){  
         if(pos>=1.e-5)  /************* Higher Matrix Product ***************/
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  
       else  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  {
       }    /* Computes the transition matrix starting at age 'age' over 
     }       'nhstepm*hstepm*stepm' months (i.e. until
     for(jk=-1; jk <=nlstate+ndeath; jk++)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       for(m=-1; m <=nlstate+ndeath; m++)       nhstepm*hstepm matrices. 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     if(i <= (int) agemax)       (typically every 2 years instead of every month which is too big 
       fprintf(ficresp,"\n");       for the memory).
     printf("\n");       Model is determined by parameters x and covariates have to be 
     }       included manually here. 
     }  
  }       */
    
   fclose(ficresp);    int i, j, d, h, k;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    double **out, cov[NCOVMAX];
   free_vector(pp,1,nlstate);    double **newm;
   
 }  /* End of Freq */    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
 /************* Waves Concatenation ***************/      for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        po[i][j][0]=(i==j ? 1.0 : 0.0);
 {      }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
      Death is a valid wave (if date is known).    for(h=1; h <=nhstepm; h++){
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      for(d=1; d <=hstepm; d++){
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        newm=savm;
      and mw[mi+1][i]. dh depends on stepm.        /* Covariates have to be included here again */
      */        cov[1]=1.;
         cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   int i, mi, m;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        for (k=1; k<=cptcovage;k++)
 float sum=0.;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
   for(i=1; i<=imx; i++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     mi=0;  
     m=firstpass;  
     while(s[m][i] <= nlstate){        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       if(s[m][i]>=1)        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         mw[++mi][i]=m;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       if(m >=lastpass)                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         break;        savm=oldm;
       else        oldm=newm;
         m++;      }
     }/* end while */      for(i=1; i<=nlstate+ndeath; i++)
     if (s[m][i] > nlstate){        for(j=1;j<=nlstate+ndeath;j++) {
       mi++;     /* Death is another wave */          po[i][j][h]=newm[i][j];
       /* if(mi==0)  never been interviewed correctly before death */          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
          /* Only death is a correct wave */           */
       mw[mi][i]=m;        }
     }    } /* end h */
     return po;
     wav[i]=mi;  }
     if(mi==0)  
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  
   }  /*************** log-likelihood *************/
   double func( double *x)
   for(i=1; i<=imx; i++){  {
     for(mi=1; mi<wav[i];mi++){    int i, ii, j, k, mi, d, kk;
       if (stepm <=0)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         dh[mi][i]=1;    double **out;
       else{    double sw; /* Sum of weights */
         if (s[mw[mi+1][i]][i] > nlstate) {    double lli; /* Individual log likelihood */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    int s1, s2;
           if(j=0) j=1;  /* Survives at least one month after exam */    double bbh, survp;
         }    long ipmx;
         else{    /*extern weight */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    /* We are differentiating ll according to initial status */
           k=k+1;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           if (j >= jmax) jmax=j;    /*for(i=1;i<imx;i++) 
           else if (j <= jmin)jmin=j;      printf(" %d\n",s[4][i]);
           sum=sum+j;    */
         }    cov[1]=1.;
         jk= j/stepm;  
         jl= j -jk*stepm;    for(k=1; k<=nlstate; k++) ll[k]=0.;
         ju= j -(jk+1)*stepm;  
         if(jl <= -ju)    if(mle==1){
           dh[mi][i]=jk;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         else        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           dh[mi][i]=jk+1;        for(mi=1; mi<= wav[i]-1; mi++){
         if(dh[mi][i]==0)          for (ii=1;ii<=nlstate+ndeath;ii++)
           dh[mi][i]=1; /* At least one step */            for (j=1;j<=nlstate+ndeath;j++){
       }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);          for(d=0; d<dh[mi][i]; d++){
 }            newm=savm;
 /*********** Tricode ****************************/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 void tricode(int *Tvar, int **nbcode, int imx)            for (kk=1; kk<=cptcovage;kk++) {
 {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int Ndum[80],ij, k, j, i;            }
   int cptcode=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for (k=0; k<79; k++) Ndum[k]=0;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (k=1; k<=7; k++) ncodemax[k]=0;            savm=oldm;
              oldm=newm;
   for (j=1; j<=cptcovn; j++) {          } /* end mult */
     for (i=1; i<=imx; i++) {        
       ij=(int)(covar[Tvar[j]][i]);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       Ndum[ij]++;          /* But now since version 0.9 we anticipate for bias at large stepm.
       if (ij > cptcode) cptcode=ij;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     }           * (in months) between two waves is not a multiple of stepm, we rounded to 
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/           * the nearest (and in case of equal distance, to the lowest) interval but now
     for (i=0; i<=cptcode; i++) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       if(Ndum[i]!=0) ncodemax[j]++;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
     }           * probability in order to take into account the bias as a fraction of the way
             * from savm to out if bh is negative or even beyond if bh is positive. bh varies
     ij=1;           * -stepm/2 to stepm/2 .
     for (i=1; i<=ncodemax[j]; i++) {           * For stepm=1 the results are the same as for previous versions of Imach.
       for (k=0; k<=79; k++) {           * For stepm > 1 the results are less biased than in previous versions. 
         if (Ndum[k] != 0) {           */
           nbcode[Tvar[j]][ij]=k;          s1=s[mw[mi][i]][i];
           ij++;          s2=s[mw[mi+1][i]][i];
         }          bbh=(double)bh[mi][i]/(double)stepm; 
         if (ij > ncodemax[j]) break;          /* bias bh is positive if real duration
       }             * is higher than the multiple of stepm and negative otherwise.
     }           */
   }            /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           if( s2 > nlstate){ 
   }            /* 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 
 /*********** Health Expectancies ****************/               die between last step unit time and current  step unit time, 
                which is also equal to probability to die before dh 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)               minus probability to die before dh-stepm . 
 {               In version up to 0.92 likelihood was computed
   /* Health expectancies */          as if date of death was unknown. Death was treated as any other
   int i, j, nhstepm, hstepm, h;          health state: the date of the interview describes the actual state
   double age, agelim,hf;          and not the date of a change in health state. The former idea was
   double ***p3mat;          to consider that at each interview the state was recorded
            (healthy, disable or death) and IMaCh was corrected; but when we
   fprintf(ficreseij,"# Health expectancies\n");          introduced the exact date of death then we should have modified
   fprintf(ficreseij,"# Age");          the contribution of an exact death to the likelihood. This new
   for(i=1; i<=nlstate;i++)          contribution is smaller and very dependent of the step unit
     for(j=1; j<=nlstate;j++)          stepm. It is no more the probability to die between last interview
       fprintf(ficreseij," %1d-%1d",i,j);          and month of death but the probability to survive from last
   fprintf(ficreseij,"\n");          interview up to one month before death multiplied by the
           probability to die within a month. Thanks to Chris
   hstepm=1*YEARM; /*  Every j years of age (in month) */          Jackson for correcting this bug.  Former versions increased
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          mortality artificially. The bad side is that we add another loop
           which slows down the processing. The difference can be up to 10%
   agelim=AGESUP;          lower mortality.
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            */
     /* nhstepm age range expressed in number of stepm */            lli=log(out[s1][s2] - savm[s1][s2]);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years = 20*12/6=40 stepm */  
     if (stepm >= YEARM) hstepm=1;          } else if  (s2==-2) {
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */            for (j=1,survp=0. ; j<=nlstate; j++) 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              survp += out[s1][j];
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            lli= survp;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          }
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            
           else if  (s2==-4) {
             for (j=3,survp=0. ; j<=nlstate; j++) 
     for(i=1; i<=nlstate;i++)              survp += out[s1][j];
       for(j=1; j<=nlstate;j++)            lli= survp;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          }
           eij[i][j][(int)age] +=p3mat[i][j][h];          
         }          else if  (s2==-5) {
                for (j=1,survp=0. ; j<=2; j++) 
     hf=1;              survp += out[s1][j];
     if (stepm >= YEARM) hf=stepm/YEARM;            lli= survp;
     fprintf(ficreseij,"%.0f",age );          }
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){  
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          else{
       }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     fprintf(ficreseij,"\n");            /*  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_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          } 
   }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 }          /*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); */
 /************ Variance ******************/          ipmx +=1;
 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)          sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* Variance of health expectancies */        } /* end of wave */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      } /* end of individual */
   double **newm;    }  else if(mle==2){
   double **dnewm,**doldm;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int i, j, nhstepm, hstepm, h;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int k, cptcode;        for(mi=1; mi<= wav[i]-1; mi++){
    double *xp;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double **gp, **gm;            for (j=1;j<=nlstate+ndeath;j++){
   double ***gradg, ***trgradg;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double ***p3mat;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double age,agelim;            }
   int theta;          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
    fprintf(ficresvij,"# Covariances of life expectancies\n");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficresvij,"# Age");            for (kk=1; kk<=cptcovage;kk++) {
   for(i=1; i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(j=1; j<=nlstate;j++)            }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   fprintf(ficresvij,"\n");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   xp=vector(1,npar);            oldm=newm;
   dnewm=matrix(1,nlstate,1,npar);          } /* end mult */
   doldm=matrix(1,nlstate,1,nlstate);        
            s1=s[mw[mi][i]][i];
   hstepm=1*YEARM; /* Every year of age */          s2=s[mw[mi+1][i]][i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          bbh=(double)bh[mi][i]/(double)stepm; 
   agelim = AGESUP;          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 (age=bage; age<=fage; age ++){ /* If stepm=6 months */          ipmx +=1;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          sw += weight[i];
     if (stepm >= YEARM) hstepm=1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        } /* end of wave */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } /* end of individual */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    }  else if(mle==3){  /* exponential inter-extrapolation */
     gp=matrix(0,nhstepm,1,nlstate);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     gm=matrix(0,nhstepm,1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
     for(theta=1; theta <=npar; theta++){          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(i=1; i<=npar; i++){ /* Computes gradient */            for (j=1;j<=nlstate+ndeath;j++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for(d=0; d<dh[mi][i]; d++){
       for(j=1; j<= nlstate; j++){            newm=savm;
         for(h=0; h<=nhstepm; h++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            for (kk=1; kk<=cptcovage;kk++) {
             gp[h][j] += prlim[i][i]*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,
                             1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(i=1; i<=npar; i++) /* Computes gradient */            savm=oldm;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            oldm=newm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            } /* end mult */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        
       for(j=1; j<= nlstate; j++){          s1=s[mw[mi][i]][i];
         for(h=0; h<=nhstepm; h++){          s2=s[mw[mi+1][i]][i];
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          bbh=(double)bh[mi][i]/(double)stepm; 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         }          ipmx +=1;
       }          sw += weight[i];
       for(j=1; j<= nlstate; j++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for(h=0; h<=nhstepm; h++){        } /* end of wave */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      } /* end of individual */
         }    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     } /* End theta */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
     for(h=0; h<=nhstepm; h++)            for (j=1;j<=nlstate+ndeath;j++){
       for(j=1; j<=nlstate;j++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(theta=1; theta <=npar; theta++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           trgradg[h][j][theta]=gradg[h][theta][j];            }
           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;
         vareij[i][j][(int)age] =0.;            for (kk=1; kk<=cptcovage;kk++) {
     for(h=0;h<=nhstepm;h++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       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]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for(i=1;i<=nlstate;i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           for(j=1;j<=nlstate;j++)            savm=oldm;
             vareij[i][j][(int)age] += doldm[i][j];            oldm=newm;
       }          } /* end mult */
     }        
     h=1;          s1=s[mw[mi][i]][i];
     if (stepm >= YEARM) h=stepm/YEARM;          s2=s[mw[mi+1][i]][i];
     fprintf(ficresvij,"%.0f ",age );          if( s2 > nlstate){ 
     for(i=1; i<=nlstate;i++)            lli=log(out[s1][s2] - savm[s1][s2]);
       for(j=1; j<=nlstate;j++){          }else{
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       }          }
     fprintf(ficresvij,"\n");          ipmx +=1;
     free_matrix(gp,0,nhstepm,1,nlstate);          sw += weight[i];
     free_matrix(gm,0,nhstepm,1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        } /* end of wave */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } /* end of individual */
   } /* End age */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_vector(xp,1,npar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   free_matrix(doldm,1,nlstate,1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
   free_matrix(dnewm,1,nlstate,1,nlstate);          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
 }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
 /************ 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)          for(d=0; d<dh[mi][i]; d++){
 {            newm=savm;
   /* Variance of prevalence limit */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            for (kk=1; kk<=cptcovage;kk++) {
   double **newm;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double **dnewm,**doldm;            }
   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");          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   for(i=1; i<=nlstate;i++)          ipmx +=1;
       fprintf(ficresvpl," %1d-%1d",i,i);          sw += weight[i];
   fprintf(ficresvpl,"\n");          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]);*/
   xp=vector(1,npar);        } /* end of wave */
   dnewm=matrix(1,nlstate,1,npar);      } /* end of individual */
   doldm=matrix(1,nlstate,1,nlstate);    } /* End of if */
      for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   hstepm=1*YEARM; /* Every year of age */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   agelim = AGESUP;    return -l;
   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;  /*************** log-likelihood *************/
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  double funcone( double *x)
     gradg=matrix(1,npar,1,nlstate);  {
     gp=vector(1,nlstate);    /* Same as likeli but slower because of a lot of printf and if */
     gm=vector(1,nlstate);    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
     for(theta=1; theta <=npar; theta++){    double **out;
       for(i=1; i<=npar; i++){ /* Computes gradient */    double lli; /* Individual log likelihood */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double llt;
       }    int s1, s2;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double bbh, survp;
       for(i=1;i<=nlstate;i++)    /*extern weight */
         gp[i] = prlim[i][i];    /* We are differentiating ll according to initial status */
        /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       for(i=1; i<=npar; i++) /* Computes gradient */    /*for(i=1;i<imx;i++) 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      printf(" %d\n",s[4][i]);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    */
       for(i=1;i<=nlstate;i++)    cov[1]=1.;
         gm[i] = prlim[i][i];  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
       for(i=1;i<=nlstate;i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     } /* End theta */      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
     trgradg =matrix(1,nlstate,1,npar);        for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
     for(j=1; j<=nlstate;j++)            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(theta=1; theta <=npar; theta++)            savm[ii][j]=(ii==j ? 1.0 : 0.0);
         trgradg[j][theta]=gradg[theta][j];          }
         for(d=0; d<dh[mi][i]; d++){
     for(i=1;i<=nlstate;i++)          newm=savm;
       varpl[i][(int)age] =0.;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          for (kk=1; kk<=cptcovage;kk++) {
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(i=1;i<=nlstate;i++)          }
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     fprintf(ficresvpl,"%.0f ",age );          savm=oldm;
     for(i=1; i<=nlstate;i++)          oldm=newm;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        } /* end mult */
     fprintf(ficresvpl,"\n");        
     free_vector(gp,1,nlstate);        s1=s[mw[mi][i]][i];
     free_vector(gm,1,nlstate);        s2=s[mw[mi+1][i]][i];
     free_matrix(gradg,1,npar,1,nlstate);        bbh=(double)bh[mi][i]/(double)stepm; 
     free_matrix(trgradg,1,nlstate,1,npar);        /* bias is positive if real duration
   } /* End age */         * is higher than the multiple of stepm and negative otherwise.
          */
   free_vector(xp,1,npar);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   free_matrix(doldm,1,nlstate,1,npar);          lli=log(out[s1][s2] - savm[s1][s2]);
   free_matrix(dnewm,1,nlstate,1,nlstate);        } else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 }        } else if(mle==2){
           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 */
         } else if(mle==3){  /* exponential inter-extrapolation */
           lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
 /***********************************************/        } else if (mle==4){  /* mle=4 no inter-extrapolation */
 /**************** Main Program *****************/          lli=log(out[s1][s2]); /* Original formula */
 /***********************************************/        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           lli=log(out[s1][s2]); /* Original formula */
 /*int main(int argc, char *argv[])*/        } /* End of if */
 int main()        ipmx +=1;
 {        sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;  /*       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]); */
   double agedeb, agefin,hf;        if(globpr){
   double agemin=1.e20, agemax=-1.e20;          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
    %10.6f %10.6f %10.6f ", \
   double fret;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   double **xi,tmp,delta;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   double dum; /* Dummy variable */            llt +=ll[k]*gipmx/gsw;
   double ***p3mat;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   int *indx;          }
   char line[MAXLINE], linepar[MAXLINE];          fprintf(ficresilk," %10.6f\n", -llt);
   char title[MAXLINE];        }
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      } /* end of wave */
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];    } /* end of individual */
   char filerest[FILENAMELENGTH];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   char fileregp[FILENAMELENGTH];    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   int firstobs=1, lastobs=10;    if(globpr==0){ /* First time we count the contributions and weights */
   int sdeb, sfin; /* Status at beginning and end */      gipmx=ipmx;
   int c,  h , cpt,l;      gsw=sw;
   int ju,jl, mi;    }
   int i1,j1, k1,jk,aa,bb, stepsize;    return -l;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  }
    
   int hstepm, nhstepm;  
   double bage, fage, age, agelim, agebase;  /*************** function likelione ***********/
   double ftolpl=FTOL;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   double **prlim;  {
   double *severity;    /* This routine should help understanding what is done with 
   double ***param; /* Matrix of parameters */       the selection of individuals/waves and
   double  *p;       to check the exact contribution to the likelihood.
   double **matcov; /* Matrix of covariance */       Plotting could be done.
   double ***delti3; /* Scale */     */
   double *delti; /* Scale */    int k;
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */    if(*globpri !=0){ /* Just counts and sums, no printings */
   double *epj, vepp;      strcpy(fileresilk,"ilk"); 
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";      strcat(fileresilk,fileres);
   char *alph[]={"a","a","b","c","d","e"}, str[4];      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   char z[1]="c", occ;        printf("Problem with resultfile: %s\n", fileresilk);
 #include <sys/time.h>        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
 #include <time.h>      }
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      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");
   /* long total_usecs;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   struct timeval start_time, end_time;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
        for(k=1; k<=nlstate; k++) 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
   printf("\nIMACH, Version 0.63");  
   printf("\nEnter the parameter file name: ");    *fretone=(*funcone)(p);
     if(*globpri !=0){
 #ifdef windows      fclose(ficresilk);
   scanf("%s",pathtot);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   getcwd(pathcd, size);      fflush(fichtm); 
   cutv(path,optionfile,pathtot,'\\');    } 
   chdir(path);    return;
   replace(pathc,path);  }
 #endif  
 #ifdef unix  
   scanf("%s",optionfile);  /*********** Maximum Likelihood Estimation ***************/
 #endif  
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 /*-------- arguments in the command line --------*/  {
     int i,j, iter;
   strcpy(fileres,"r");    double **xi;
   strcat(fileres, optionfile);    double fret;
     double fretone; /* Only one call to likelihood */
   /*---------arguments file --------*/    /*  char filerespow[FILENAMELENGTH];*/
     xi=matrix(1,npar,1,npar);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    for (i=1;i<=npar;i++)
     printf("Problem with optionfile %s\n",optionfile);      for (j=1;j<=npar;j++)
     goto end;        xi[i][j]=(i==j ? 1.0 : 0.0);
   }    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
   strcpy(filereso,"o");    strcat(filerespow,fileres);
   strcat(filereso,fileres);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   if((ficparo=fopen(filereso,"w"))==NULL) {      printf("Problem with resultfile: %s\n", filerespow);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   }    }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
   /* Reads comments: lines beginning with '#' */    for (i=1;i<=nlstate;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){      for(j=1;j<=nlstate+ndeath;j++)
     ungetc(c,ficpar);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fgets(line, MAXLINE, ficpar);    fprintf(ficrespow,"\n");
     puts(line);  
     fputs(line,ficparo);    powell(p,xi,npar,ftol,&iter,&fret,func);
   }  
   ungetc(c,ficpar);    fclose(ficrespow);
     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   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);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   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;  /**** Computes Hessian and covariance matrix ***/
   else {  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     j=0;  {
     j=nbocc(model,'+');    double  **a,**y,*x,pd;
     cptcovn=j+1;    double **hess;
   }    int i, j,jk;
     int *indx;
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
      double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   /* Read guess parameters */    void lubksb(double **a, int npar, int *indx, double b[]) ;
   /* Reads comments: lines beginning with '#' */    void ludcmp(double **a, int npar, int *indx, double *d) ;
   while((c=getc(ficpar))=='#' && c!= EOF){    double gompertz(double p[]);
     ungetc(c,ficpar);    hess=matrix(1,npar,1,npar);
     fgets(line, MAXLINE, ficpar);  
     puts(line);    printf("\nCalculation of the hessian matrix. Wait...\n");
     fputs(line,ficparo);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   }    for (i=1;i<=npar;i++){
   ungetc(c,ficpar);      printf("%d",i);fflush(stdout);
        fprintf(ficlog,"%d",i);fflush(ficlog);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);     
     for(i=1; i <=nlstate; i++)       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     for(j=1; j <=nlstate+ndeath-1; j++){      
       fscanf(ficpar,"%1d%1d",&i1,&j1);      /*  printf(" %f ",p[i]);
       fprintf(ficparo,"%1d%1d",i1,j1);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       printf("%1d%1d",i,j);    }
       for(k=1; k<=ncovmodel;k++){    
         fscanf(ficpar," %lf",&param[i][j][k]);    for (i=1;i<=npar;i++) {
         printf(" %lf",param[i][j][k]);      for (j=1;j<=npar;j++)  {
         fprintf(ficparo," %lf",param[i][j][k]);        if (j>i) { 
       }          printf(".%d%d",i,j);fflush(stdout);
       fscanf(ficpar,"\n");          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       printf("\n");          hess[i][j]=hessij(p,delti,i,j,func,npar);
       fprintf(ficparo,"\n");          
     }          hess[j][i]=hess[i][j];    
            /*printf(" %lf ",hess[i][j]);*/
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;        }
   p=param[1][1];      }
      }
   /* Reads comments: lines beginning with '#' */    printf("\n");
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficlog,"\n");
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     puts(line);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     fputs(line,ficparo);    
   }    a=matrix(1,npar,1,npar);
   ungetc(c,ficpar);    y=matrix(1,npar,1,npar);
     x=vector(1,npar);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    indx=ivector(1,npar);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    for (i=1;i<=npar;i++)
   for(i=1; i <=nlstate; i++){      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     for(j=1; j <=nlstate+ndeath-1; j++){    ludcmp(a,npar,indx,&pd);
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);    for (j=1;j<=npar;j++) {
       fprintf(ficparo,"%1d%1d",i1,j1);      for (i=1;i<=npar;i++) x[i]=0;
       for(k=1; k<=ncovmodel;k++){      x[j]=1;
         fscanf(ficpar,"%le",&delti3[i][j][k]);      lubksb(a,npar,indx,x);
         printf(" %le",delti3[i][j][k]);      for (i=1;i<=npar;i++){ 
         fprintf(ficparo," %le",delti3[i][j][k]);        matcov[i][j]=x[i];
       }      }
       fscanf(ficpar,"\n");    }
       printf("\n");  
       fprintf(ficparo,"\n");    printf("\n#Hessian matrix#\n");
     }    fprintf(ficlog,"\n#Hessian matrix#\n");
   }    for (i=1;i<=npar;i++) { 
   delti=delti3[1][1];      for (j=1;j<=npar;j++) { 
          printf("%.3e ",hess[i][j]);
   /* Reads comments: lines beginning with '#' */        fprintf(ficlog,"%.3e ",hess[i][j]);
   while((c=getc(ficpar))=='#' && c!= EOF){      }
     ungetc(c,ficpar);      printf("\n");
     fgets(line, MAXLINE, ficpar);      fprintf(ficlog,"\n");
     puts(line);    }
     fputs(line,ficparo);  
   }    /* Recompute Inverse */
   ungetc(c,ficpar);    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   matcov=matrix(1,npar,1,npar);    ludcmp(a,npar,indx,&pd);
   for(i=1; i <=npar; i++){  
     fscanf(ficpar,"%s",&str);    /*  printf("\n#Hessian matrix recomputed#\n");
     printf("%s",str);  
     fprintf(ficparo,"%s",str);    for (j=1;j<=npar;j++) {
     for(j=1; j <=i; j++){      for (i=1;i<=npar;i++) x[i]=0;
       fscanf(ficpar," %le",&matcov[i][j]);      x[j]=1;
       printf(" %.5le",matcov[i][j]);      lubksb(a,npar,indx,x);
       fprintf(ficparo," %.5le",matcov[i][j]);      for (i=1;i<=npar;i++){ 
     }        y[i][j]=x[i];
     fscanf(ficpar,"\n");        printf("%.3e ",y[i][j]);
     printf("\n");        fprintf(ficlog,"%.3e ",y[i][j]);
     fprintf(ficparo,"\n");      }
   }      printf("\n");
   for(i=1; i <=npar; i++)      fprintf(ficlog,"\n");
     for(j=i+1;j<=npar;j++)    }
       matcov[i][j]=matcov[j][i];    */
      
   printf("\n");    free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
    if(mle==1){    free_ivector(indx,1,npar);
     /*-------- data file ----------*/    free_matrix(hess,1,npar,1,npar);
     if((ficres =fopen(fileres,"w"))==NULL) {  
       printf("Problem with resultfile: %s\n", fileres);goto end;  
     }  }
     fprintf(ficres,"#%s\n",version);  
      /*************** hessian matrix ****************/
     if((fic=fopen(datafile,"r"))==NULL)    {  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
       printf("Problem with datafile: %s\n", datafile);goto end;  {
     }    int i;
     int l=1, lmax=20;
     n= lastobs;    double k1,k2;
     severity = vector(1,maxwav);    double p2[NPARMAX+1];
     outcome=imatrix(1,maxwav+1,1,n);    double res;
     num=ivector(1,n);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     moisnais=vector(1,n);    double fx;
     annais=vector(1,n);    int k=0,kmax=10;
     moisdc=vector(1,n);    double l1;
     andc=vector(1,n);  
     agedc=vector(1,n);    fx=func(x);
     cod=ivector(1,n);    for (i=1;i<=npar;i++) p2[i]=x[i];
     weight=vector(1,n);    for(l=0 ; l <=lmax; l++){
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      l1=pow(10,l);
     mint=matrix(1,maxwav,1,n);      delts=delt;
     anint=matrix(1,maxwav,1,n);      for(k=1 ; k <kmax; k=k+1){
     s=imatrix(1,maxwav+1,1,n);        delt = delta*(l1*k);
     adl=imatrix(1,maxwav+1,1,n);            p2[theta]=x[theta] +delt;
     tab=ivector(1,NCOVMAX);        k1=func(p2)-fx;
     ncodemax=ivector(1,8);        p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
     i=1;        /*res= (k1-2.0*fx+k2)/delt/delt; */
     while (fgets(line, MAXLINE, fic) != NULL)    {        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       if ((i >= firstobs) && (i <=lastobs)) {        
          #ifdef DEBUG
         for (j=maxwav;j>=1;j--){        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        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);
           strcpy(line,stra);  #endif
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         }          k=kmax;
                }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          k=kmax; l=lmax*10.;
         }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          delts=delt;
         }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      }
         for (j=ncov;j>=1;j--){    }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    delti[theta]=delts;
         }    return res; 
         num[i]=atol(stra);    
   }
         /*printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]),  (mint[5][i]), (anint[5][i]), (s[5][i]),  (mint[6][i]), (anint[6][i]), (s[6][i]));*/  
   double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
         i=i+1;  {
       }    int i;
     }    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
     /*scanf("%d",i);*/    double p2[NPARMAX+1];
   imx=i-1; /* Number of individuals */    int k;
   
   /* Calculation of the number of parameter from char model*/    fx=func(x);
   Tvar=ivector(1,8);        for (k=1; k<=2; k++) {
          for (i=1;i<=npar;i++) p2[i]=x[i];
   if (strlen(model) >1){      p2[thetai]=x[thetai]+delti[thetai]/k;
     j=0;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     j=nbocc(model,'+');      k1=func(p2)-fx;
     cptcovn=j+1;    
          p2[thetai]=x[thetai]+delti[thetai]/k;
     strcpy(modelsav,model);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     if (j==0) {      k2=func(p2)-fx;
       cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb);    
     }      p2[thetai]=x[thetai]-delti[thetai]/k;
     else {      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       for(i=j; i>=1;i--){      k3=func(p2)-fx;
         cutv(stra,strb,modelsav,'+');    
         if (strchr(strb,'*')) {      p2[thetai]=x[thetai]-delti[thetai]/k;
           cutv(strd,strc,strb,'*');      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           cutv(strb,stre,strc,'V');Tvar[i+1]=ncov+1;      k4=func(p2)-fx;
           cutv(strb,strc,strd,'V');      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
           for (k=1; k<=lastobs;k++)  #ifdef DEBUG
             covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      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);
         else {cutv(strd,strc,strb,'V');  #endif
         Tvar[i+1]=atoi(strc);    }
         }    return res;
         strcpy(modelsav,stra);    }
       }  
       cutv(strd,strc,stra,'V');  /************** Inverse of matrix **************/
       Tvar[1]=atoi(strc);  void ludcmp(double **a, int n, int *indx, double *d) 
     }  { 
   }    int i,imax,j,k; 
   /*printf("tvar=%d ",Tvar[1]);    double big,dum,sum,temp; 
   scanf("%d ",i);*/    double *vv; 
     fclose(fic);   
     vv=vector(1,n); 
     if (weightopt != 1) { /* Maximisation without weights*/    *d=1.0; 
       for(i=1;i<=n;i++) weight[i]=1.0;    for (i=1;i<=n;i++) { 
     }      big=0.0; 
     /*-calculation of age at interview from date of interview and age at death -*/      for (j=1;j<=n;j++) 
     agev=matrix(1,maxwav,1,imx);        if ((temp=fabs(a[i][j])) > big) big=temp; 
          if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     for (i=1; i<=imx; i++)  {      vv[i]=1.0/big; 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    } 
       for(m=1; (m<= maxwav); m++){    for (j=1;j<=n;j++) { 
         if(s[m][i] >0){      for (i=1;i<j;i++) { 
           if (s[m][i] == nlstate+1) {        sum=a[i][j]; 
             if(agedc[i]>0)        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
               if(moisdc[i]!=99 && andc[i]!=9999)        a[i][j]=sum; 
               agev[m][i]=agedc[i];      } 
             else{      big=0.0; 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      for (i=j;i<=n;i++) { 
               agev[m][i]=-1;        sum=a[i][j]; 
             }        for (k=1;k<j;k++) 
           }          sum -= a[i][k]*a[k][j]; 
           else if(s[m][i] !=9){ /* Should no more exist */        a[i][j]=sum; 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
             if(mint[m][i]==99 || anint[m][i]==9999)          big=dum; 
               agev[m][i]=1;          imax=i; 
             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);*/      if (j != imax) { 
             }        for (k=1;k<=n;k++) { 
             else if(agev[m][i] >agemax){          dum=a[imax][k]; 
               agemax=agev[m][i];          a[imax][k]=a[j][k]; 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/          a[j][k]=dum; 
             }        } 
             /*agev[m][i]=anint[m][i]-annais[i];*/        *d = -(*d); 
             /*   agev[m][i] = age[i]+2*m;*/        vv[imax]=vv[j]; 
           }      } 
           else { /* =9 */      indx[j]=imax; 
             agev[m][i]=1;      if (a[j][j] == 0.0) a[j][j]=TINY; 
             s[m][i]=-1;      if (j != n) { 
           }        dum=1.0/(a[j][j]); 
         }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         else /*= 0 Unknown */      } 
           agev[m][i]=1;    } 
       }    free_vector(vv,1,n);  /* Doesn't work */
      ;
     }  } 
     for (i=1; i<=imx; i++)  {  
       for(m=1; (m<= maxwav); m++){  void lubksb(double **a, int n, int *indx, double b[]) 
         if (s[m][i] > (nlstate+ndeath)) {  { 
           printf("Error: Wrong value in nlstate or ndeath\n");      int i,ii=0,ip,j; 
           goto end;    double sum; 
         }   
       }    for (i=1;i<=n;i++) { 
     }      ip=indx[i]; 
       sum=b[ip]; 
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);      b[ip]=b[i]; 
       if (ii) 
     free_vector(severity,1,maxwav);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     free_imatrix(outcome,1,maxwav+1,1,n);      else if (sum) ii=i; 
     free_vector(moisnais,1,n);      b[i]=sum; 
     free_vector(annais,1,n);    } 
     free_matrix(mint,1,maxwav,1,n);    for (i=n;i>=1;i--) { 
     free_matrix(anint,1,maxwav,1,n);      sum=b[i]; 
     free_vector(moisdc,1,n);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     free_vector(andc,1,n);      b[i]=sum/a[i][i]; 
     } 
      } 
     wav=ivector(1,imx);  
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  /************ Frequencies ********************/
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  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 */
     /* Concatenates waves */    
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     int first;
     double ***freq; /* Frequencies */
 Tcode=ivector(1,100);    double *pp, **prop;
    nbcode=imatrix(1,nvar,1,8);      double pos,posprop, k2, dateintsum=0,k2cpt=0;
    ncodemax[1]=1;    FILE *ficresp;
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);    char fileresp[FILENAMELENGTH];
      
    codtab=imatrix(1,100,1,10);    pp=vector(1,nlstate);
    h=0;    prop=matrix(1,nlstate,iagemin,iagemax+3);
    m=pow(2,cptcovn);    strcpy(fileresp,"p");
      strcat(fileresp,fileres);
    for(k=1;k<=cptcovn; k++){    if((ficresp=fopen(fileresp,"w"))==NULL) {
      for(i=1; i <=(m/pow(2,k));i++){      printf("Problem with prevalence resultfile: %s\n", fileresp);
        for(j=1; j <= ncodemax[k]; j++){      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
          for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){      exit(0);
            h++;    }
            if (h>m) h=1;codtab[h][k]=j;    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
          }    j1=0;
        }    
      }    j=cptcoveff;
    }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
    /*for(i=1; i <=m ;i++){    first=1;
      for(k=1; k <=cptcovn; k++){  
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);    for(k1=1; k1<=j;k1++){
      }      for(i1=1; i1<=ncodemax[k1];i1++){
      printf("\n");        j1++;
    }*/        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
    /*scanf("%d",i);*/          scanf("%d", i);*/
            for (i=-5; i<=nlstate+ndeath; i++)  
    /* Calculates basic frequencies. Computes observed prevalence at single age          for (jk=-5; jk<=nlstate+ndeath; jk++)  
        and prints on file fileres'p'. */            for(m=iagemin; m <= iagemax+3; m++)
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);              freq[i][jk][m]=0;
   
       for (i=1; i<=nlstate; i++)  
   /*scanf("%d ",i);*/        for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
         
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        dateintsum=0;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        k2cpt=0;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for (i=1; i<=imx; i++) {
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          bool=1;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          if  (cptcovn>0) {
                for (z1=1; z1<=cptcoveff; z1++) 
     /* For Powell, parameters are in a vector p[] starting at p[1]              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */                bool=0;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          }
              if (bool==1){
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
                  /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     /*--------- results files --------------*/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     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(agev[m][i]==1) agev[m][i]=iagemax+2;
                    if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
    jk=1;                if (m<lastpass) {
    fprintf(ficres,"# Parameters\n");                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
    printf("# Parameters\n");                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
    for(i=1,jk=1; i <=nlstate; i++){                }
      for(k=1; k <=(nlstate+ndeath); k++){                
        if (k != i)                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
          {                  dateintsum=dateintsum+k2;
            printf("%d%d ",i,k);                  k2cpt++;
            fprintf(ficres,"%1d%1d ",i,k);                }
            for(j=1; j <=ncovmodel; j++){                /*}*/
              printf("%f ",p[jk]);            }
              fprintf(ficres,"%f ",p[jk]);          }
              jk++;        }
            }         
            printf("\n");        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
            fprintf(ficres,"\n");  fprintf(ficresp, "#Local time at start: %s", strstart);
          }        if  (cptcovn>0) {
      }          fprintf(ficresp, "\n#********** Variable "); 
    }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\n#");
     /* Computing hessian and covariance matrix */        }
     ftolhess=ftol; /* Usually correct */        for(i=1; i<=nlstate;i++) 
     hesscov(matcov, p, npar, delti, ftolhess, func);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     fprintf(ficres,"# Scales\n");        fprintf(ficresp, "\n");
     printf("# Scales\n");        
      for(i=1,jk=1; i <=nlstate; i++){        for(i=iagemin; i <= iagemax+3; i++){
       for(j=1; j <=nlstate+ndeath; j++){          if(i==iagemax+3){
         if (j!=i) {            fprintf(ficlog,"Total");
           fprintf(ficres,"%1d%1d",i,j);          }else{
           printf("%1d%1d",i,j);            if(first==1){
           for(k=1; k<=ncovmodel;k++){              first=0;
             printf(" %.5e",delti[jk]);              printf("See log file for details...\n");
             fprintf(ficres," %.5e",delti[jk]);            }
             jk++;            fprintf(ficlog,"Age %d", i);
           }          }
           printf("\n");          for(jk=1; jk <=nlstate ; jk++){
           fprintf(ficres,"\n");            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         }              pp[jk] += freq[jk][m][i]; 
       }          }
       }          for(jk=1; jk <=nlstate ; jk++){
                for(m=-1, pos=0; m <=0 ; m++)
     k=1;              pos += freq[jk][m][i];
     fprintf(ficres,"# Covariance\n");            if(pp[jk]>=1.e-10){
     printf("# Covariance\n");              if(first==1){
     for(i=1;i<=npar;i++){              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       /*  if (k>nlstate) k=1;              }
       i1=(i-1)/(ncovmodel*nlstate)+1;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);            }else{
       printf("%s%d%d",alph[k],i1,tab[i]);*/              if(first==1)
       fprintf(ficres,"%3d",i);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       printf("%3d",i);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       for(j=1; j<=i;j++){            }
         fprintf(ficres," %.5e",matcov[i][j]);          }
         printf(" %.5e",matcov[i][j]);  
       }          for(jk=1; jk <=nlstate ; jk++){
       fprintf(ficres,"\n");            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       printf("\n");              pp[jk] += freq[jk][m][i];
       k++;          }       
     }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
                pos += pp[jk];
     while((c=getc(ficpar))=='#' && c!= EOF){            posprop += prop[jk][i];
       ungetc(c,ficpar);          }
       fgets(line, MAXLINE, ficpar);          for(jk=1; jk <=nlstate ; jk++){
       puts(line);            if(pos>=1.e-5){
       fputs(line,ficparo);              if(first==1)
     }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     ungetc(c,ficpar);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
              }else{
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);              if(first==1)
                    printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     if (fage <= 2) {              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       bage = agemin;            }
       fage = agemax;            if( i <= iagemax){
     }              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                /*probs[i][jk][j1]= pp[jk]/pos;*/
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 /*------------ gnuplot -------------*/              }
 chdir(pathcd);              else
   if((ficgp=fopen("graph.plt","w"))==NULL) {                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     printf("Problem with file graph.gp");goto end;            }
   }          }
 #ifdef windows          
   fprintf(ficgp,"cd \"%s\" \n",pathc);          for(jk=-1; jk <=nlstate+ndeath; jk++)
 #endif            for(m=-1; m <=nlstate+ndeath; m++)
 m=pow(2,cptcovn);              if(freq[jk][m][i] !=0 ) {
                if(first==1)
  /* 1eme*/                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   for (cpt=1; cpt<= nlstate ; cpt ++) {                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
    for (k1=1; k1<= m ; k1 ++) {              }
           if(i <= iagemax)
 #ifdef windows            fprintf(ficresp,"\n");
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);          if(first==1)
 #endif            printf("Others in log...\n");
 #ifdef unix          fprintf(ficlog,"\n");
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);        }
 #endif      }
     }
 for (i=1; i<= nlstate ; i ++) {    dateintmean=dateintsum/k2cpt; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");   
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fclose(ficresp);
 }    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    free_vector(pp,1,nlstate);
     for (i=1; i<= nlstate ; i ++) {    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /* End of Freq */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  }
 }  
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  /************ Prevalence ********************/
      for (i=1; i<= nlstate ; i ++) {  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  {  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
 }         in each health status at the date of interview (if between dateprev1 and dateprev2).
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));       We still use firstpass and lastpass as another selection.
 #ifdef unix    */
 fprintf(ficgp,"\nset ter gif small size 400,300");   
 #endif    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    double ***freq; /* Frequencies */
    }    double *pp, **prop;
   }    double pos,posprop; 
   /*2 eme*/    double  y2; /* in fractional years */
     int iagemin, iagemax;
   for (k1=1; k1<= m ; k1 ++) {  
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    iagemin= (int) agemin;
        iagemax= (int) agemax;
     for (i=1; i<= nlstate+1 ; i ++) {    /*pp=vector(1,nlstate);*/
       k=2*i;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       for (j=1; j<= nlstate+1 ; j ++) {    j1=0;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    
   else fprintf(ficgp," \%%*lf (\%%*lf)");    j=cptcoveff;
 }      if (cptcovn<1) {j=1;ncodemax[1]=1;}
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    for(k1=1; k1<=j;k1++){
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      for(i1=1; i1<=ncodemax[k1];i1++){
       for (j=1; j<= nlstate+1 ; j ++) {        j1++;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        
         else fprintf(ficgp," \%%*lf (\%%*lf)");        for (i=1; i<=nlstate; i++)  
 }            for(m=iagemin; m <= iagemax+3; m++)
       fprintf(ficgp,"\" t\"\" w l 0,");            prop[i][m]=0.0;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);       
       for (j=1; j<= nlstate+1 ; j ++) {        for (i=1; i<=imx; i++) { /* Each individual */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          bool=1;
   else fprintf(ficgp," \%%*lf (\%%*lf)");          if  (cptcovn>0) {
 }              for (z1=1; z1<=cptcoveff; z1++) 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       else fprintf(ficgp,"\" t\"\" w l 0,");                bool=0;
     }          } 
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          if (bool==1) { 
   }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
                y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   /*3eme*/              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
    for (k1=1; k1<= m ; k1 ++) {                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     for (cpt=1; cpt<= nlstate ; cpt ++) {                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); 
       k=2+nlstate*(cpt-1);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       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);                  /*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]]);*/
       for (i=1; i< nlstate ; i ++) {                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);                  prop[s[m][i]][iagemax+3] += weight[i]; 
       }                } 
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              }
     }            } /* end selection of waves */
    }          }
          }
   /* CV preval stat */        for(i=iagemin; i <= iagemax+3; i++){  
     for (k1=1; k1<= m ; k1 ++) {          
     for (cpt=1; cpt<nlstate ; cpt ++) {          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       k=3;            posprop += prop[jk][i]; 
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);          } 
       for (i=1; i< nlstate ; i ++)  
         fprintf(ficgp,"+$%d",k+i+1);          for(jk=1; jk <=nlstate ; jk++){     
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            if( i <=  iagemax){ 
                    if(posprop>=1.e-5){ 
       l=3+(nlstate+ndeath)*cpt;                probs[i][jk][j1]= prop[jk][i]/posprop;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);              } 
       for (i=1; i< nlstate ; i ++) {            } 
         l=3+(nlstate+ndeath)*cpt;          }/* end jk */ 
         fprintf(ficgp,"+$%d",l+i+1);        }/* end i */ 
       }      } /* end i1 */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      } /* end k1 */
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    
     }    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   }    /*free_vector(pp,1,nlstate);*/
      free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   /* proba elementaires */  }  /* End of prevalence */
   for(i=1,jk=1; i <=nlstate; i++){  
     for(k=1; k <=(nlstate+ndeath); k++){  /************* Waves Concatenation ***************/
       if (k != i) {  
         /*  fprintf(ficgp,"%1d%1d ",i,k);*/  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
         for(j=1; j <=ncovmodel; j++){  {
           fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
           jk++;       Death is a valid wave (if date is known).
           fprintf(ficgp,"\n");       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       }       and mw[mi+1][i]. dh depends on stepm.
     }       */
   }  
   for(jk=1; jk <=m; jk++) {    int i, mi, m;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   for(i=1; i <=nlstate; i++) {       double sum=0., jmean=0.;*/
     for(k=1; k <=(nlstate+ndeath); k++){    int first;
       if (k != i) {    int j, k=0,jk, ju, jl;
         fprintf(ficgp," exp(a%d%d+b%d%d*x",i,k,i,k);    double sum=0.;
         for(j=3; j <=ncovmodel; j++)    first=0;
           fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    jmin=1e+5;
         fprintf(ficgp,")/(1");    jmax=-1;
         for(k1=1; k1 <=(nlstate+ndeath); k1++)    jmean=0.;
           if (k1 != i) {    for(i=1; i<=imx; i++){
             fprintf(ficgp,"+exp(a%d%d+b%d%d*x",i,k1,i,k1);      mi=0;
             for(j=3; j <=ncovmodel; j++)      m=firstpass;
               fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      while(s[m][i] <= nlstate){
             fprintf(ficgp,")");        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
           }          mw[++mi][i]=m;
         fprintf(ficgp,") t \"p%d%d\" ", i,k);        if(m >=lastpass)
       if ((i+k)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          break;
       }        else
     }          m++;
   }      }/* end while */
 fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        if (s[m][i] > nlstate){
   }        mi++;     /* Death is another wave */
          /* if(mi==0)  never been interviewed correctly before death */
  fclose(ficgp);           /* Only death is a correct wave */
         mw[mi][i]=m;
     chdir(path);      }
     free_matrix(agev,1,maxwav,1,imx);  
     free_ivector(wav,1,imx);      wav[i]=mi;
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      if(mi==0){
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        nbwarn++;
            if(first==0){
     free_imatrix(s,1,maxwav+1,1,n);          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
              first=1;
            }
     free_ivector(num,1,n);        if(first==1){
     free_vector(agedc,1,n);          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
     free_vector(weight,1,n);        }
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      } /* end mi==0 */
     fclose(ficparo);    } /* End individuals */
     fclose(ficres);  
    }    for(i=1; i<=imx; i++){
          for(mi=1; mi<wav[i];mi++){
    /*________fin mle=1_________*/        if (stepm <=0)
              dh[mi][i]=1;
         else{
            if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     /* No more information from the sample is required now */            if (agedc[i] < 2*AGESUP) {
   /* Reads comments: lines beginning with '#' */              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   while((c=getc(ficpar))=='#' && c!= EOF){              if(j==0) j=1;  /* Survives at least one month after exam */
     ungetc(c,ficpar);              else if(j<0){
     fgets(line, MAXLINE, ficpar);                nberr++;
     puts(line);                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]);
     fputs(line,ficparo);                j=1; /* Temporary Dangerous patch */
   }                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
   ungetc(c,ficpar);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                  fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               }
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);              k=k+1;
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);              if (j >= jmax) jmax=j;
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);              if (j <= jmin) jmin=j;
 /*--------- index.htm --------*/              sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   if((fichtm=fopen("index.htm","w"))==NULL)    {              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     printf("Problem with index.htm \n");goto end;            }
   }          }
           else{
  fprintf(fichtm,"<body><ul> Imach, Version 0.63<hr> <li>Outputs files<br><br>\n            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\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]); */
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>  
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>            k=k+1;
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>            if (j >= jmax) jmax=j;
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>            else if (j <= jmin)jmin=j;
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>            /*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]);*/
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>            if(j<0){
         - 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);              nberr++;
               printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
  fprintf(fichtm," <li>Graphs</li>\n<p>");              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]);
             }
  m=cptcovn;            sum=sum+j;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          }
           jk= j/stepm;
  j1=0;          jl= j -jk*stepm;
  for(k1=1; k1<=m;k1++){          ju= j -(jk+1)*stepm;
    for(i1=1; i1<=ncodemax[k1];i1++){          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
        j1++;            if(jl==0){
        if (cptcovn > 0) {              dh[mi][i]=jk;
          fprintf(fichtm,"<hr>************ Results for covariates");              bh[mi][i]=0;
          for (cpt=1; cpt<=cptcovn;cpt++)            }else{ /* We want a negative bias in order to only have interpolation ie
            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);                    * at the price of an extra matrix product in likelihood */
          fprintf(fichtm," ************\n<hr>");              dh[mi][i]=jk+1;
        }              bh[mi][i]=ju;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>            }
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              }else{
        for(cpt=1; cpt<nlstate;cpt++){            if(jl <= -ju){
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>              dh[mi][i]=jk;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);              bh[mi][i]=jl;       /* bias is positive if real duration
        }                                   * is higher than the multiple of stepm and negative otherwise.
     for(cpt=1; cpt<=nlstate;cpt++) {                                   */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident            }
 interval) in state (%d): v%s%d%d.gif <br>            else{
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);                dh[mi][i]=jk+1;
      }              bh[mi][i]=ju;
      for(cpt=1; cpt<=nlstate;cpt++) {            }
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>            if(dh[mi][i]==0){
 <img src=\"ex%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);              dh[mi][i]=1; /* At least one step */
      }              bh[mi][i]=ju; /* At least one step */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and              /*  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);*/
 health expectancies in states (1) and (2): e%s%d.gif<br>            }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          } /* end if mle */
 fprintf(fichtm,"\n</body>");        }
    }      } /* end wave */
  }    }
 fclose(fichtm);    jmean=sum/k;
     printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   /*--------------- Prevalence limit --------------*/    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     }
   strcpy(filerespl,"pl");  
   strcat(filerespl,fileres);  /*********** Tricode ****************************/
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  void tricode(int *Tvar, int **nbcode, int imx)
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  {
   }    
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    int Ndum[20],ij=1, k, j, i, maxncov=19;
   fprintf(ficrespl,"#Prevalence limit\n");    int cptcode=0;
   fprintf(ficrespl,"#Age ");    cptcoveff=0; 
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);   
   fprintf(ficrespl,"\n");    for (k=0; k<maxncov; k++) Ndum[k]=0;
      for (k=1; k<=7; k++) ncodemax[k]=0;
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                                 modality*/ 
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        Ndum[ij]++; /*store the modality */
   k=0;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   agebase=agemin;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   agelim=agemax;                                         Tvar[j]. If V=sex and male is 0 and 
   ftolpl=1.e-10;                                         female is 1, then  cptcode=1.*/
   i1=cptcovn;      }
   if (cptcovn < 1){i1=1;}  
       for (i=0; i<=cptcode; i++) {
   for(cptcov=1;cptcov<=i1;cptcov++){        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 */
     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]);*/      ij=1; 
         fprintf(ficrespl,"\n#****** ");      for (i=1; i<=ncodemax[j]; i++) {
         for(j=1;j<=cptcovn;j++)        for (k=0; k<= maxncov; k++) {
           fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);          if (Ndum[k] != 0) {
         fprintf(ficrespl,"******\n");            nbcode[Tvar[j]][ij]=k; 
                    /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
         for (age=agebase; age<=agelim; age++){            
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            ij++;
           fprintf(ficrespl,"%.0f",age );          }
           for(i=1; i<=nlstate;i++)          if (ij > ncodemax[j]) break; 
           fprintf(ficrespl," %.5f", prlim[i][i]);        }  
           fprintf(ficrespl,"\n");      } 
         }    }  
       }  
     }   for (k=0; k< maxncov; k++) Ndum[k]=0;
   fclose(ficrespl);  
   /*------------- h Pij x at various ages ------------*/   for (i=1; i<=ncovmodel-2; i++) { 
       /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);     ij=Tvar[i];
   if((ficrespij=fopen(filerespij,"w"))==NULL) {     Ndum[ij]++;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;   }
   }  
   printf("Computing pij: result on file '%s' \n", filerespij);   ij=1;
     for (i=1; i<= maxncov; i++) {
   stepsize=(int) (stepm+YEARM-1)/YEARM;     if((Ndum[i]!=0) && (i<=ncovcol)){
   if (stepm<=24) stepsize=2;       Tvaraff[ij]=i; /*For printing */
        ij++;
   agelim=AGESUP;     }
   hstepm=stepsize*YEARM; /* Every year of age */   }
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */   
     cptcoveff=ij-1; /*Number of simple covariates*/
   k=0;  }
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  /*********** Health Expectancies ****************/
       k=k+1;  
         fprintf(ficrespij,"\n#****** ");  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov,char strstart[] )
         for(j=1;j<=cptcovn;j++)  
           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);  {
         fprintf(ficrespij,"******\n");    /* Health expectancies */
            int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    double age, agelim, hf;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double ***p3mat,***varhe;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    double **dnewm,**doldm;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double *xp;
           oldm=oldms;savm=savms;    double **gp, **gm;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double ***gradg, ***trgradg;
           fprintf(ficrespij,"# Age");    int theta;
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
               fprintf(ficrespij," %1d-%1d",i,j);    xp=vector(1,npar);
           fprintf(ficrespij,"\n");    dnewm=matrix(1,nlstate*nlstate,1,npar);
           for (h=0; h<=nhstepm; h++){    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    
             for(i=1; i<=nlstate;i++)    fprintf(ficreseij,"# Local time at start: %s", strstart);
               for(j=1; j<=nlstate+ndeath;j++)    fprintf(ficreseij,"# Health expectancies\n");
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    fprintf(ficreseij,"# Age");
             fprintf(ficrespij,"\n");    for(i=1; i<=nlstate;i++)
           }      for(j=1; j<=nlstate;j++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
           fprintf(ficrespij,"\n");    fprintf(ficreseij,"\n");
         }  
     }    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
   fclose(ficrespij);    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
   /*---------- Health expectancies and variances ------------*/     * 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
   strcpy(filerest,"t");     * we are calculating an estimate of the Life Expectancy assuming a linear 
   strcat(filerest,fileres);     * progression in between and thus overestimating or underestimating according
   if((ficrest=fopen(filerest,"w"))==NULL) {     * to the curvature of the survival function. If, for the same date, we 
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;     * 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 
   printf("Computing Total LEs with variances: file '%s' \n", filerest);     * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   
   strcpy(filerese,"e");    /* For example we decided to compute the life expectancy with the smallest unit */
   strcat(filerese,fileres);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   if((ficreseij=fopen(filerese,"w"))==NULL) {       nhstepm is the number of hstepm from age to agelim 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);       nstepm is the number of stepm from age to agelin. 
   }       Look at hpijx to understand the reason of that which relies in memory size
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
  strcpy(fileresv,"v");       survival function given by stepm (the optimization length). Unfortunately it
   strcat(fileresv,fileres);       means that if the survival funtion is printed only each two years of age and if
   if((ficresvij=fopen(fileresv,"w"))==NULL) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);       results. So we changed our mind and took the option of the best precision.
   }    */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
   k=0;    agelim=AGESUP;
   for(cptcov=1;cptcov<=i1;cptcov++){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      /* nhstepm age range expressed in number of stepm */
       k=k+1;      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       fprintf(ficrest,"\n#****** ");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       for(j=1;j<=cptcovn;j++)      /* if (stepm >= YEARM) hstepm=1;*/
         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       fprintf(ficrest,"******\n");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       fprintf(ficreseij,"\n#****** ");      gp=matrix(0,nhstepm,1,nlstate*nlstate);
       for(j=1;j<=cptcovn;j++)      gm=matrix(0,nhstepm,1,nlstate*nlstate);
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       fprintf(ficresvij,"\n#****** ");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
       for(j=1;j<=cptcovn;j++)   
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  
       fprintf(ficresvij,"******\n");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      /* Computing  Variances of health expectancies */
       oldm=oldms;savm=savms;  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);         for(theta=1; theta <=npar; theta++){
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        for(i=1; i<=npar; i++){ 
       oldm=oldms;savm=savms;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        }
              hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);        cptj=0;
       fprintf(ficrest,"\n");        for(j=1; j<= nlstate; j++){
                  for(i=1; i<=nlstate; i++){
       hf=1;            cptj=cptj+1;
       if (stepm >= YEARM) hf=stepm/YEARM;            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
       epj=vector(1,nlstate+1);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       for(age=bage; age <=fage ;age++){            }
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          }
         fprintf(ficrest," %.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]*hf*eij[i][j][(int)age];        for(i=1; i<=npar; i++) 
           }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           epj[nlstate+1] +=epj[j];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         }        
         for(i=1, vepp=0.;i <=nlstate;i++)        cptj=0;
           for(j=1;j <=nlstate;j++)        for(j=1; j<= nlstate; j++){
             vepp += vareij[i][j][(int)age];          for(i=1;i<=nlstate;i++){
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));            cptj=cptj+1;
         for(j=1;j <=nlstate;j++){            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));  
         }              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
         fprintf(ficrest,"\n");            }
       }          }
     }        }
   }        for(j=1; j<= nlstate*nlstate; j++)
                  for(h=0; h<=nhstepm-1; h++){
  fclose(ficreseij);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
  fclose(ficresvij);          }
   fclose(ficrest);       } 
   fclose(ficpar);     
   free_vector(epj,1,nlstate+1);  /* End theta */
   /*scanf("%d ",i); */  
        trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   /*------- Variance limit prevalence------*/    
        for(h=0; h<=nhstepm-1; h++)
 strcpy(fileresvpl,"vpl");        for(j=1; j<=nlstate*nlstate;j++)
   strcat(fileresvpl,fileres);          for(theta=1; theta <=npar; theta++)
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {            trgradg[h][j][theta]=gradg[h][theta][j];
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);       
     exit(0);  
   }       for(i=1;i<=nlstate*nlstate;i++)
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        for(j=1;j<=nlstate*nlstate;j++)
           varhe[i][j][(int)age] =0.;
  k=0;  
  for(cptcov=1;cptcov<=i1;cptcov++){       printf("%d|",(int)age);fflush(stdout);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
      k=k+1;       for(h=0;h<=nhstepm-1;h++){
      fprintf(ficresvpl,"\n#****** ");        for(k=0;k<=nhstepm-1;k++){
      for(j=1;j<=cptcovn;j++)          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
        fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
      fprintf(ficresvpl,"******\n");          for(i=1;i<=nlstate*nlstate;i++)
                  for(j=1;j<=nlstate*nlstate;j++)
      varpl=matrix(1,nlstate,(int) bage, (int) fage);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
      oldm=oldms;savm=savms;        }
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      }
    }      /* Computing expectancies */
  }      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
   fclose(ficresvpl);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   /*---------- End : free ----------------*/            
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
        fprintf(ficreseij,"%3.0f",age );
        cptj=0;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      for(i=1; i<=nlstate;i++)
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        for(j=1; j<=nlstate;j++){
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);          cptj++;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
          }
   free_matrix(matcov,1,npar,1,npar);      fprintf(ficreseij,"\n");
   free_vector(delti,1,npar);     
        free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   printf("End of Imach\n");      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      }
   /* 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("\n");
   /*printf("Total time was %d uSec.\n", total_usecs);*/    fprintf(ficlog,"\n");
   /*------ End -----------*/  
     free_vector(xp,1,npar);
  end:    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
 #ifdef windows    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
  chdir(pathcd);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
 #endif  }
  system("wgnuplot graph.plt");  
   /************ Variance ******************/
 #ifdef windows  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[])
   while (z[0] != 'q') {  {
     chdir(pathcd);    /* Variance of health expectancies */
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     scanf("%s",z);    /* double **newm;*/
     if (z[0] == 'c') system("./imach");    double **dnewm,**doldm;
     else if (z[0] == 'e') {    double **dnewmp,**doldmp;
       chdir(path);    int i, j, nhstepm, hstepm, h, nstepm ;
       system("index.htm");    int k, cptcode;
     }    double *xp;
     else if (z[0] == 'q') exit(0);    double **gp, **gm;  /* for var eij */
   }    double ***gradg, ***trgradg; /*for var eij */
 #endif    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);
     fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     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);
    fprintf(ficresvij, "#Local time at start: %s", strstart);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
     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;
     fprintf(ficresvpl, "#Local time at start: %s", strstart); 
     fprintf(ficresvpl,"# Standard deviation of 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);
     fprintf(ficresprob, "#Local time at start: %s", strstart);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     fprintf(ficresprobcov, "#Local time at start: %s", strstart);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor, "#Local time at start: %s", strstart);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# 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_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - Life expectancies by age and initial health status (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i]==1 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i]==0 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         if (wav[i]>1 & agecens[i]>15) {
           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 jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     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]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
         for(j=0; line[j] != '\n';j++){  /* Untabifies line */
           if(line[j] == '\t')
             line[j] = ' ';
         }
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of 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);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (j=1; j<=lastpass; j++)
           if (s[j][i]>nlstate) {
             dcwave[i]=j;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];agecens[i]=1.; 
           if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
           cens[i]=1;
           
           if (ageexmed[i]<1) cens[i]=-1;
           if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
   
       p[1]=0.1; p[2]=0.1;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow-mort"); 
     strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
     /*  for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     */
     fprintf(ficrespow,"\n");
   
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM,delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
   lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
      
        for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
      
         for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
   
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
   
    tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
          }
      
      
          printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
   
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
   
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
   
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficrespl, "#Local time at start: %s", strstart);
       fprintf(ficrespl,"#Stable prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       fprintf(ficrespij, "#Local time at start: %s", strstart);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /*---------- Health expectancies and variances ------------*/
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total LEs with variances: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficreseij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
           }
   
           fprintf(ficrest, "#Local time at start: %s", strstart);
           fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficreseij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of stable prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
   #ifndef UNIX
     /*  strcpy(plotcmd,"\""); */
   #endif
     strcpy(plotcmd,pathimach);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     strcat(plotcmd,GNUPLOTPROGRAM);
   #ifndef UNIX
     strcat(plotcmd,".exe");
     /*  strcat(plotcmd,"\"");*/
   #endif
     if(stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
     }
   
   #ifndef UNIX
     strcpy(plotcmd,"\"");
   #endif
     strcat(plotcmd,pathimach);
     strcat(plotcmd,GNUPLOTPROGRAM);
   #ifndef UNIX
     strcat(plotcmd,".exe");
     strcat(plotcmd,"\"");
   #endif
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.3  
changed lines
  Added in v.1.108


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