Diff for /imach/src/imach.c between versions 1.3 and 1.110

version 1.3, 2001/05/02 17:21:42 version 1.110, 2006/01/25 00:51:50
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 1.110  2006/01/25 00:51:50  brouard
   individuals from different ages are interviewed on their health status    (Module): Lots of cleaning and bugs added (Gompertz)
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.109  2006/01/24 19:37:15  brouard
   Health expectancies are computed from the transistions observed between    (Module): Comments (lines starting with a #) are allowed in data.
   waves and are computed for each degree of severity of disability (number  
   of life states). More degrees you consider, more time is necessary to    Revision 1.108  2006/01/19 18:05:42  lievre
   reach the Maximum Likelihood of the parameters involved in the model.    Gnuplot problem appeared...
   The simplest model is the multinomial logistic model where pij is    To be fixed
   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 1.107  2006/01/19 16:20:37  brouard
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Test existence of gnuplot in imach path
   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 1.106  2006/01/19 13:24:36  brouard
     *Covariates have to be included here again* invites you to do it.    Some cleaning and links added in html output
   More covariates you add, less is the speed of the convergence.  
     Revision 1.105  2006/01/05 20:23:19  lievre
   The advantage that this computer programme claims, comes from that if the    *** empty log message ***
   delay between waves is not identical for each individual, or if some  
   individual missed an interview, the information is not rounded or lost, but    Revision 1.104  2005/09/30 16:11:43  lievre
   taken into account using an interpolation or extrapolation.    (Module): sump fixed, loop imx fixed, and simplifications.
   hPijx is the probability to be    (Module): If the status is missing at the last wave but we know
   observed in state i at age x+h conditional to the observed state i at age    that the person is alive, then we can code his/her status as -2
   x. The delay 'h' can be split into an exact number (nh*stepm) of    (instead of missing=-1 in earlier versions) and his/her
   unobserved intermediate  states. This elementary transition (by month or    contributions to the likelihood is 1 - Prob of dying from last
   quarter trimester, semester or year) is model as a multinomial logistic.    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    the healthy state at last known wave). Version is 0.98
   and the contribution of each individual to the likelihood is simply hPijx.  
     Revision 1.103  2005/09/30 15:54:49  lievre
   Also this programme outputs the covariance matrix of the parameters but also    (Module): sump fixed, loop imx fixed, and simplifications.
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.102  2004/09/15 17:31:30  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Add the possibility to read data file including tab characters.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.101  2004/09/15 10:38:38  brouard
   from the European Union.    Fix on curr_time
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.100  2004/07/12 18:29:06  brouard
   can be accessed at http://euroreves.ined.fr/imach .    Add version for Mac OS X. Just define UNIX in Makefile
   **********************************************************************/  
      Revision 1.99  2004/06/05 08:57:40  brouard
 #include <math.h>    *** empty log message ***
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.98  2004/05/16 15:05:56  brouard
 #include <unistd.h>    New version 0.97 . First attempt to estimate force of mortality
     directly from the data i.e. without the need of knowing the health
 #define MAXLINE 256    state at each age, but using a Gompertz model: log u =a + b*age .
 #define FILENAMELENGTH 80    This is the basic analysis of mortality and should be done before any
 /*#define DEBUG*/    other analysis, in order to test if the mortality estimated from the
 #define windows    cross-longitudinal survey is different from the mortality estimated
     from other sources like vital statistic data.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    The same imach parameter file can be used but the option for mle should be -3.
   
 #define NINTERVMAX 8    Agnès, who wrote this part of the code, tried to keep most of the
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    former routines in order to include the new code within the former code.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    The output is very simple: only an estimate of the intercept and of
 #define MAXN 20000    the slope with 95% confident intervals.
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Current limitations:
 #define AGEBASE 40    A) Even if you enter covariates, i.e. with the
     model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
     B) There is no computation of Life Expectancy nor Life Table.
 int nvar;  
 static int cptcov;    Revision 1.97  2004/02/20 13:25:42  lievre
 int cptcovn;    Version 0.96d. Population forecasting command line is (temporarily)
 int npar=NPARMAX;    suppressed.
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.96  2003/07/15 15:38:55  brouard
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     rewritten within the same printf. Workaround: many printfs.
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.95  2003/07/08 07:54:34  brouard
 int mle, weightopt;    * imach.c (Repository):
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Repository): Using imachwizard code to output a more meaningful covariance
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    matrix (cov(a12,c31) instead of numbers.
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.94  2003/06/27 13:00:02  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    Just cleaning
 FILE *ficgp, *fichtm;  
 FILE *ficreseij;    Revision 1.93  2003/06/25 16:33:55  brouard
   char filerese[FILENAMELENGTH];    (Module): On windows (cygwin) function asctime_r doesn't
  FILE  *ficresvij;    exist so I changed back to asctime which exists.
   char fileresv[FILENAMELENGTH];    (Module): Version 0.96b
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
   
     Revision 1.91  2003/06/25 15:30:29  brouard
 #define NR_END 1    * imach.c (Repository): Duplicated warning errors corrected.
 #define FREE_ARG char*    (Repository): Elapsed time after each iteration is now output. It
 #define FTOL 1.0e-10    helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
 #define NRANSI    concerning matrix of covariance. It has extension -cov.htm.
 #define ITMAX 200  
     Revision 1.90  2003/06/24 12:34:15  brouard
 #define TOL 2.0e-4    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 #define CGOLD 0.3819660    of the covariance matrix to be input.
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.89  2003/06/24 12:30:52  brouard
     (Module): Some bugs corrected for windows. Also, when
 #define GOLD 1.618034    mle=-1 a template is output in file "or"mypar.txt with the design
 #define GLIMIT 100.0    of the covariance matrix to be input.
 #define TINY 1.0e-20  
     Revision 1.88  2003/06/23 17:54:56  brouard
 static double maxarg1,maxarg2;    * 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 FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.87  2003/06/18 12:26:01  brouard
      Version 0.96
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
 static double sqrarg;    routine fileappend.
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
 int imx;    current date of interview. It may happen when the death was just
 int stepm;    prior to the death. In this case, dh was negative and likelihood
 /* Stepm, step in month: minimum step interpolation*/    was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
 int m,nb;    interview.
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax;    (Repository): Because some people have very long ID (first column)
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    we changed int to long in num[] and we added a new lvector for
 double **pmmij;    memory allocation. But we also truncated to 8 characters (left
     truncation)
 double *weight;    (Repository): No more line truncation errors.
 int **s; /* Status */  
 double *agedc, **covar, idx;    Revision 1.84  2003/06/13 21:44:43  brouard
 int **nbcode, *Tcode, *Tvar, **codtab;    * imach.c (Repository): Replace "freqsummary" at a correct
     place. It differs from routine "prevalence" which may be called
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    many times. Probs is memory consuming and must be used with
 double ftolhess; /* Tolerance for computing hessian */    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 /******************************************/    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
 void replace(char *s, char*t)  
 {    Revision 1.82  2003/06/05 15:57:20  brouard
   int i;    Add log in  imach.c and  fullversion number is now printed.
   int lg=20;  
   i=0;  */
   lg=strlen(t);  /*
   for(i=0; i<= lg; i++) {     Interpolated Markov Chain
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Short summary of the programme:
   }    
 }    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 int nbocc(char *s, char occ)    first survey ("cross") where individuals from different ages are
 {    interviewed on their health status or degree of disability (in the
   int i,j=0;    case of a health survey which is our main interest) -2- at least a
   int lg=20;    second wave of interviews ("longitudinal") which measure each change
   i=0;    (if any) in individual health status.  Health expectancies are
   lg=strlen(s);    computed from the time spent in each health state according to a
   for(i=0; i<= lg; i++) {    model. More health states you consider, more time is necessary to reach the
   if  (s[i] == occ ) j++;    Maximum Likelihood of the parameters involved in the model.  The
   }    simplest model is the multinomial logistic model where pij is the
   return j;    probability to be observed in state j at the second wave
 }    conditional to be observed in state i at the first wave. Therefore
     the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 void cutv(char *u,char *v, char*t, char occ)    'age' is age and 'sex' is a covariate. If you want to have a more
 {    complex model than "constant and age", you should modify the program
   int i,lg,j,p;    where the markup *Covariates have to be included here again* invites
   i=0;    you to do it.  More covariates you add, slower the
   for(j=0; j<=strlen(t)-1; j++) {    convergence.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
   lg=strlen(t);    identical for each individual. Also, if a individual missed an
   for(j=0; j<p; j++) {    intermediate interview, the information is lost, but taken into
     (u[j] = t[j]);    account using an interpolation or extrapolation.  
     u[p]='\0';  
   }    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
    for(j=0; j<= lg; j++) {    split into an exact number (nh*stepm) of unobserved intermediate
     if (j>=(p+1))(v[j-p-1] = t[j]);    states. This elementary transition (by month, quarter,
   }    semester or year) is modelled as a multinomial logistic.  The hPx
 }    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
 /********************** nrerror ********************/    hPijx.
   
 void nrerror(char error_text[])    Also this programme outputs the covariance matrix of the parameters but also
 {    of the life expectancies. It also computes the stable prevalence. 
   fprintf(stderr,"ERREUR ...\n");    
   fprintf(stderr,"%s\n",error_text);    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   exit(1);             Institut national d'études démographiques, Paris.
 }    This software have been partly granted by Euro-REVES, a concerted action
 /*********************** vector *******************/    from the European Union.
 double *vector(int nl, int nh)    It is copyrighted identically to a GNU software product, ie programme and
 {    software can be distributed freely for non commercial use. Latest version
   double *v;    can be accessed at http://euroreves.ined.fr/imach .
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   return v-nl+NR_END;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 }    
     **********************************************************************/
 /************************ free vector ******************/  /*
 void free_vector(double*v, int nl, int nh)    main
 {    read parameterfile
   free((FREE_ARG)(v+nl-NR_END));    read datafile
 }    concatwav
     freqsummary
 /************************ivector *******************************/    if (mle >= 1)
 int *ivector(long nl,long nh)      mlikeli
 {    print results files
   int *v;    if mle==1 
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));       computes hessian
   if (!v) nrerror("allocation failure in ivector");    read end of parameter file: agemin, agemax, bage, fage, estepm
   return v-nl+NR_END;        begin-prev-date,...
 }    open gnuplot file
     open html file
 /******************free ivector **************************/    stable prevalence
 void free_ivector(int *v, long nl, long nh)     for age prevalim()
 {    h Pij x
   free((FREE_ARG)(v+nl-NR_END));    variance of p varprob
 }    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
 /******************* imatrix *******************************/    Variance-covariance of DFLE
 int **imatrix(long nrl, long nrh, long ncl, long nch)    prevalence()
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */     movingaverage()
 {    varevsij() 
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    if popbased==1 varevsij(,popbased)
   int **m;    total life expectancies
      Variance of stable prevalence
   /* allocate pointers to rows */   end
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  */
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  
   m -= nrl;  
     
    #include <math.h>
   /* allocate rows and set pointers to them */  #include <stdio.h>
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #include <stdlib.h>
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #include <string.h>
   m[nrl] += NR_END;  #include <unistd.h>
   m[nrl] -= ncl;  
    #include <limits.h>
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  #include <sys/types.h>
    #include <sys/stat.h>
   /* return pointer to array of pointers to rows */  #include <errno.h>
   return m;  extern int errno;
 }  
   /* #include <sys/time.h> */
 /****************** free_imatrix *************************/  #include <time.h>
 void free_imatrix(m,nrl,nrh,ncl,nch)  #include "timeval.h"
       int **m;  
       long nch,ncl,nrh,nrl;  /* #include <libintl.h> */
      /* free an int matrix allocated by imatrix() */  /* #define _(String) gettext (String) */
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #define MAXLINE 256
   free((FREE_ARG) (m+nrl-NR_END));  
 }  #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 /******************* matrix *******************************/  #define FILENAMELENGTH 132
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   double **m;  
   #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  #define NINTERVMAX 8
   m -= nrl;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define NCOVMAX 8 /* Maximum number of covariates */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define MAXN 20000
   m[nrl] += NR_END;  #define YEARM 12. /* Number of months per year */
   m[nrl] -= ncl;  #define AGESUP 130
   #define AGEBASE 40
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   return m;  #ifdef UNIX
 }  #define DIRSEPARATOR '/'
   #define CHARSEPARATOR "/"
 /*************************free matrix ************************/  #define ODIRSEPARATOR '\\'
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  #else
 {  #define DIRSEPARATOR '\\'
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define CHARSEPARATOR "\\"
   free((FREE_ARG)(m+nrl-NR_END));  #define ODIRSEPARATOR '/'
 }  #endif
   
 /******************* ma3x *******************************/  /* $Id$ */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  /* $State$ */
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
   double ***m;  char fullversion[]="$Revision$ $Date$"; 
   int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int nvar;
   if (!m) nrerror("allocation failure 1 in matrix()");  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   m += NR_END;  int npar=NPARMAX;
   m -= nrl;  int nlstate=2; /* Number of live states */
   int ndeath=1; /* Number of dead states */
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int popbased=0;
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav; /* Maxim number of waves */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int jmin, jmax; /* min, max spacing between 2 waves */
   int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  int gipmx, gsw; /* Global variables on the number of contributions 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");                     to the likelihood and the sum of weights (done by funcone)*/
   m[nrl][ncl] += NR_END;  int mle, weightopt;
   m[nrl][ncl] -= nll;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   for (j=ncl+1; j<=nch; j++)  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     m[nrl][j]=m[nrl][j-1]+nlay;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
               * wave mi and wave mi+1 is not an exact multiple of stepm. */
   for (i=nrl+1; i<=nrh; i++) {  double jmean; /* Mean space between 2 waves */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  double **oldm, **newm, **savm; /* Working pointers to matrices */
     for (j=ncl+1; j<=nch; j++)  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       m[i][j]=m[i][j-1]+nlay;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   }  FILE *ficlog, *ficrespow;
   return m;  int globpr; /* Global variable for printing or not */
 }  double fretone; /* Only one call to likelihood */
   long ipmx; /* Number of contributions */
 /*************************free ma3x ************************/  double sw; /* Sum of weights */
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  char filerespow[FILENAMELENGTH];
 {  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  FILE *ficresilk;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   free((FREE_ARG)(m+nrl-NR_END));  FILE *ficresprobmorprev;
 }  FILE *fichtm, *fichtmcov; /* Html File */
   FILE *ficreseij;
 /***************** f1dim *************************/  char filerese[FILENAMELENGTH];
 extern int ncom;  FILE  *ficresvij;
 extern double *pcom,*xicom;  char fileresv[FILENAMELENGTH];
 extern double (*nrfunc)(double []);  FILE  *ficresvpl;
    char fileresvpl[FILENAMELENGTH];
 double f1dim(double x)  char title[MAXLINE];
 {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   int j;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   double f;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   double *xt;  char command[FILENAMELENGTH];
    int  outcmd=0;
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  char filelog[FILENAMELENGTH]; /* Log file */
   return f;  char filerest[FILENAMELENGTH];
 }  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 {  
   int iter;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   double a,b,d,etemp;  struct timezone tzp;
   double fu,fv,fw,fx;  extern int gettimeofday();
   double ftemp;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   double p,q,r,tol1,tol2,u,v,w,x,xm;  long time_value;
   double e=0.0;  extern long time();
    char strcurr[80], strfor[80];
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);  char *endptr;
   x=w=v=bx;  long lval;
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {  #define NR_END 1
     xm=0.5*(a+b);  #define FREE_ARG char*
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  #define FTOL 1.0e-10
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  #define NRANSI 
 #ifdef DEBUG  #define ITMAX 200 
     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);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  #define TOL 2.0e-4 
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  #define CGOLD 0.3819660 
       *xmin=x;  #define ZEPS 1.0e-10 
       return fx;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     }  
     ftemp=fu;  #define GOLD 1.618034 
     if (fabs(e) > tol1) {  #define GLIMIT 100.0 
       r=(x-w)*(fx-fv);  #define TINY 1.0e-20 
       q=(x-v)*(fx-fw);  
       p=(x-v)*q-(x-w)*r;  static double maxarg1,maxarg2;
       q=2.0*(q-r);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       if (q > 0.0) p = -p;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       q=fabs(q);    
       etemp=e;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       e=d;  #define rint(a) floor(a+0.5)
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  static double sqrarg;
       else {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
         d=p/q;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
         u=x+d;  int agegomp= AGEGOMP;
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  int imx; 
       }  int stepm=1;
     } else {  /* Stepm, step in month: minimum step interpolation*/
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  int estepm;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     fu=(*f)(u);  
     if (fu <= fx) {  int m,nb;
       if (u >= x) a=x; else b=x;  long *num;
       SHFT(v,w,x,u)  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
         SHFT(fv,fw,fx,fu)  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
         } else {  double **pmmij, ***probs;
           if (u < x) a=u; else b=u;  double *ageexmed,*agecens;
           if (fu <= fw || w == x) {  double dateintmean=0;
             v=w;  
             w=u;  double *weight;
             fv=fw;  int **s; /* Status */
             fw=fu;  double *agedc, **covar, idx;
           } else if (fu <= fv || v == x || v == w) {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
             v=u;  double *lsurv, *lpop, *tpop;
             fv=fu;  
           }  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
         }  double ftolhess; /* Tolerance for computing hessian */
   }  
   nrerror("Too many iterations in brent");  /**************** split *************************/
   *xmin=x;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   return fx;  {
 }    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
        the name of the file (name), its extension only (ext) and its first part of the name (finame)
 /****************** mnbrak ***********************/    */ 
     char  *ss;                            /* pointer */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    int   l1, l2;                         /* length counters */
             double (*func)(double))  
 {    l1 = strlen(path );                   /* length of path */
   double ulim,u,r,q, dum;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   double fu;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
      if ( ss == NULL ) {                   /* no directory, so determine current directory */
   *fa=(*func)(*ax);      strcpy( name, path );               /* we got the fullname name because no directory */
   *fb=(*func)(*bx);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   if (*fb > *fa) {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     SHFT(dum,*ax,*bx,dum)      /* get current working directory */
       SHFT(dum,*fb,*fa,dum)      /*    extern  char* getcwd ( char *buf , int len);*/
       }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   *cx=(*bx)+GOLD*(*bx-*ax);        return( GLOCK_ERROR_GETCWD );
   *fc=(*func)(*cx);      }
   while (*fb > *fc) {      /* got dirc from getcwd*/
     r=(*bx-*ax)*(*fb-*fc);      printf(" DIRC = %s \n",dirc);
     q=(*bx-*cx)*(*fb-*fa);    } else {                              /* strip direcotry from path */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      ss++;                               /* after this, the filename */
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));      l2 = strlen( ss );                  /* length of filename */
     ulim=(*bx)+GLIMIT*(*cx-*bx);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     if ((*bx-u)*(u-*cx) > 0.0) {      strcpy( name, ss );         /* save file name */
       fu=(*func)(u);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     } else if ((*cx-u)*(u-ulim) > 0.0) {      dirc[l1-l2] = 0;                    /* add zero */
       fu=(*func)(u);      printf(" DIRC2 = %s \n",dirc);
       if (fu < *fc) {    }
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    /* We add a separator at the end of dirc if not exists */
           SHFT(*fb,*fc,fu,(*func)(u))    l1 = strlen( dirc );                  /* length of directory */
           }    if( dirc[l1-1] != DIRSEPARATOR ){
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      dirc[l1] =  DIRSEPARATOR;
       u=ulim;      dirc[l1+1] = 0; 
       fu=(*func)(u);      printf(" DIRC3 = %s \n",dirc);
     } else {    }
       u=(*cx)+GOLD*(*cx-*bx);    ss = strrchr( name, '.' );            /* find last / */
       fu=(*func)(u);    if (ss >0){
     }      ss++;
     SHFT(*ax,*bx,*cx,u)      strcpy(ext,ss);                     /* save extension */
       SHFT(*fa,*fb,*fc,fu)      l1= strlen( name);
       }      l2= strlen(ss)+1;
 }      strncpy( finame, name, l1-l2);
       finame[l1-l2]= 0;
 /*************** linmin ************************/    }
   
 int ncom;    return( 0 );                          /* we're done */
 double *pcom,*xicom;  }
 double (*nrfunc)(double []);  
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  /******************************************/
 {  
   double brent(double ax, double bx, double cx,  void replace_back_to_slash(char *s, char*t)
                double (*f)(double), double tol, double *xmin);  {
   double f1dim(double x);    int i;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    int lg=0;
               double *fc, double (*func)(double));    i=0;
   int j;    lg=strlen(t);
   double xx,xmin,bx,ax;    for(i=0; i<= lg; i++) {
   double fx,fb,fa;      (s[i] = t[i]);
        if (t[i]== '\\') s[i]='/';
   ncom=n;    }
   pcom=vector(1,n);  }
   xicom=vector(1,n);  
   nrfunc=func;  int nbocc(char *s, char occ)
   for (j=1;j<=n;j++) {  {
     pcom[j]=p[j];    int i,j=0;
     xicom[j]=xi[j];    int lg=20;
   }    i=0;
   ax=0.0;    lg=strlen(s);
   xx=1.0;    for(i=0; i<= lg; i++) {
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    if  (s[i] == occ ) j++;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    }
 #ifdef DEBUG    return j;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  }
 #endif  
   for (j=1;j<=n;j++) {  void cutv(char *u,char *v, char*t, char occ)
     xi[j] *= xmin;  {
     p[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')
   free_vector(xicom,1,n);       gives u="abcedf" and v="ghi2j" */
   free_vector(pcom,1,n);    int i,lg,j,p=0;
 }    i=0;
     for(j=0; j<=strlen(t)-1; j++) {
 /*************** powell ************************/      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    }
             double (*func)(double []))  
 {    lg=strlen(t);
   void linmin(double p[], double xi[], int n, double *fret,    for(j=0; j<p; j++) {
               double (*func)(double []));      (u[j] = t[j]);
   int i,ibig,j;    }
   double del,t,*pt,*ptt,*xit;       u[p]='\0';
   double fp,fptt;  
   double *xits;     for(j=0; j<= lg; j++) {
   pt=vector(1,n);      if (j>=(p+1))(v[j-p-1] = t[j]);
   ptt=vector(1,n);    }
   xit=vector(1,n);  }
   xits=vector(1,n);  
   *fret=(*func)(p);  /********************** nrerror ********************/
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  void nrerror(char error_text[])
     fp=(*fret);  {
     ibig=0;    fprintf(stderr,"ERREUR ...\n");
     del=0.0;    fprintf(stderr,"%s\n",error_text);
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    exit(EXIT_FAILURE);
     for (i=1;i<=n;i++)  }
       printf(" %d %.12f",i, p[i]);  /*********************** vector *******************/
     printf("\n");  double *vector(int nl, int nh)
     for (i=1;i<=n;i++) {  {
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    double *v;
       fptt=(*fret);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 #ifdef DEBUG    if (!v) nrerror("allocation failure in vector");
       printf("fret=%lf \n",*fret);    return v-nl+NR_END;
 #endif  }
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  /************************ free vector ******************/
       if (fabs(fptt-(*fret)) > del) {  void free_vector(double*v, int nl, int nh)
         del=fabs(fptt-(*fret));  {
         ibig=i;    free((FREE_ARG)(v+nl-NR_END));
       }  }
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));  /************************ivector *******************************/
       for (j=1;j<=n;j++) {  int *ivector(long nl,long nh)
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  {
         printf(" x(%d)=%.12e",j,xit[j]);    int *v;
       }    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       for(j=1;j<=n;j++)    if (!v) nrerror("allocation failure in ivector");
         printf(" p=%.12e",p[j]);    return v-nl+NR_END;
       printf("\n");  }
 #endif  
     }  /******************free ivector **************************/
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  void free_ivector(int *v, long nl, long nh)
 #ifdef DEBUG  {
       int k[2],l;    free((FREE_ARG)(v+nl-NR_END));
       k[0]=1;  }
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  /************************lvector *******************************/
       for (j=1;j<=n;j++)  long *lvector(long nl,long nh)
         printf(" %.12e",p[j]);  {
       printf("\n");    long *v;
       for(l=0;l<=1;l++) {    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
         for (j=1;j<=n;j++) {    if (!v) nrerror("allocation failure in ivector");
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    return v-nl+NR_END;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  }
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  /******************free lvector **************************/
       }  void free_lvector(long *v, long nl, long nh)
 #endif  {
     free((FREE_ARG)(v+nl-NR_END));
   }
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  /******************* imatrix *******************************/
       free_vector(ptt,1,n);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       free_vector(pt,1,n);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       return;  { 
     }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    int **m; 
     for (j=1;j<=n;j++) {    
       ptt[j]=2.0*p[j]-pt[j];    /* allocate pointers to rows */ 
       xit[j]=p[j]-pt[j];    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       pt[j]=p[j];    if (!m) nrerror("allocation failure 1 in matrix()"); 
     }    m += NR_END; 
     fptt=(*func)(ptt);    m -= nrl; 
     if (fptt < fp) {    
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    
       if (t < 0.0) {    /* allocate rows and set pointers to them */ 
         linmin(p,xit,n,fret,func);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
         for (j=1;j<=n;j++) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
           xi[j][ibig]=xi[j][n];    m[nrl] += NR_END; 
           xi[j][n]=xit[j];    m[nrl] -= ncl; 
         }    
 #ifdef DEBUG    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    
         for(j=1;j<=n;j++)    /* return pointer to array of pointers to rows */ 
           printf(" %.12e",xit[j]);    return m; 
         printf("\n");  } 
 #endif  
       }  /****************** free_imatrix *************************/
     }  void free_imatrix(m,nrl,nrh,ncl,nch)
   }        int **m;
 }        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
 /**** Prevalence limit ****************/  { 
     free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    free((FREE_ARG) (m+nrl-NR_END)); 
 {  } 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  
      matrix by transitions matrix until convergence is reached */  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
   int i, ii,j,k;  {
   double min, max, maxmin, maxmax,sumnew=0.;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   double **matprod2();    double **m;
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double agefin, delaymax=50 ; /* Max number of years to converge */    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
   for (ii=1;ii<=nlstate+ndeath;ii++)    m -= nrl;
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    m[nrl] += NR_END;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    m[nrl] -= ncl;
     newm=savm;  
     /* Covariates have to be included here again */    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     cov[1]=1.;    return m;
     cov[2]=agefin;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     if (cptcovn>0){     */
       for (k=1; k<=cptcovn;k++) {cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];/*printf("Tcode[ij]=%d nbcode=%d\n",Tcode[ij],nbcode[k][Tcode[ij]]);*/}  }
     }  
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  /*************************free matrix ************************/
   void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     savm=oldm;  {
     oldm=newm;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     maxmax=0.;    free((FREE_ARG)(m+nrl-NR_END));
     for(j=1;j<=nlstate;j++){  }
       min=1.;  
       max=0.;  /******************* ma3x *******************************/
       for(i=1; i<=nlstate; i++) {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
         sumnew=0;  {
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
         prlim[i][j]= newm[i][j]/(1-sumnew);    double ***m;
         max=FMAX(max,prlim[i][j]);  
         min=FMIN(min,prlim[i][j]);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       }    if (!m) nrerror("allocation failure 1 in matrix()");
       maxmin=max-min;    m += NR_END;
       maxmax=FMAX(maxmax,maxmin);    m -= nrl;
     }  
     if(maxmax < ftolpl){    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       return prlim;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     }    m[nrl] += NR_END;
   }    m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 /*************** transition probabilities **********/  
     m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 {    m[nrl][ncl] += NR_END;
   double s1, s2;    m[nrl][ncl] -= nll;
   /*double t34;*/    for (j=ncl+1; j<=nch; j++) 
   int i,j,j1, nc, ii, jj;      m[nrl][j]=m[nrl][j-1]+nlay;
     
     for(i=1; i<= nlstate; i++){    for (i=nrl+1; i<=nrh; i++) {
     for(j=1; j<i;j++){      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      for (j=ncl+1; j<=nch; j++) 
         /*s2 += param[i][j][nc]*cov[nc];*/        m[i][j]=m[i][j-1]+nlay;
         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);*/    return m; 
       }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       ps[i][j]=s2;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    */
     }  }
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /*************************free ma3x ************************/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  {
       }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       ps[i][j]=s2;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     }    free((FREE_ARG)(m+nrl-NR_END));
   }  }
   for(i=1; i<= nlstate; i++){  
      s1=0;  /*************** function subdirf ***********/
     for(j=1; j<i; j++)  char *subdirf(char fileres[])
       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,"/"); /* Add to the right */
     for(j=1; j<i; j++)    strcat(tmpout,fileres);
       ps[i][j]= exp(ps[i][j])*ps[i][i];    return tmpout;
     for(j=i+1; j<=nlstate+ndeath; j++)  }
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  /*************** function subdirf2 ***********/
   } /* end i */  char *subdirf2(char fileres[], char *preop)
   {
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    
     for(jj=1; jj<= nlstate+ndeath; jj++){    /* Caution optionfilefiname is hidden */
       ps[ii][jj]=0;    strcpy(tmpout,optionfilefiname);
       ps[ii][ii]=1;    strcat(tmpout,"/");
     }    strcat(tmpout,preop);
   }    strcat(tmpout,fileres);
     return tmpout;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  }
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  /*************** function subdirf3 ***********/
    }  char *subdirf3(char fileres[], char *preop, char *preop2)
     printf("\n ");  {
     }    
     printf("\n ");printf("%lf ",cov[2]);*/    /* Caution optionfilefiname is hidden */
 /*    strcpy(tmpout,optionfilefiname);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    strcat(tmpout,"/");
   goto end;*/    strcat(tmpout,preop);
     return ps;    strcat(tmpout,preop2);
 }    strcat(tmpout,fileres);
     return tmpout;
 /**************** Product of 2 matrices ******************/  }
   
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  /***************** f1dim *************************/
 {  extern int ncom; 
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  extern double *pcom,*xicom;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  extern double (*nrfunc)(double []); 
   /* in, b, out are matrice of pointers which should have been initialized   
      before: only the contents of out is modified. The function returns  double f1dim(double x) 
      a pointer to pointers identical to out */  { 
   long i, j, k;    int j; 
   for(i=nrl; i<= nrh; i++)    double f;
     for(k=ncolol; k<=ncoloh; k++)    double *xt; 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)   
         out[i][k] +=in[i][j]*b[j][k];    xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   return out;    f=(*nrfunc)(xt); 
 }    free_vector(xt,1,ncom); 
     return f; 
   } 
 /************* Higher Matrix Product ***************/  
   /*****************brent *************************/
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
 {  { 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    int iter; 
      duration (i.e. until    double a,b,d,etemp;
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    double fu,fv,fw,fx;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    double ftemp;
      (typically every 2 years instead of every month which is too big).    double p,q,r,tol1,tol2,u,v,w,x,xm; 
      Model is determined by parameters x and covariates have to be    double e=0.0; 
      included manually here.   
     a=(ax < cx ? ax : cx); 
      */    b=(ax > cx ? ax : cx); 
     x=w=v=bx; 
   int i, j, d, h, k;    fw=fv=fx=(*f)(x); 
   double **out, cov[NCOVMAX];    for (iter=1;iter<=ITMAX;iter++) { 
   double **newm;      xm=0.5*(a+b); 
       tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   /* Hstepm could be zero and should return the unit matrix */      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   for (i=1;i<=nlstate+ndeath;i++)      printf(".");fflush(stdout);
     for (j=1;j<=nlstate+ndeath;j++){      fprintf(ficlog,".");fflush(ficlog);
       oldm[i][j]=(i==j ? 1.0 : 0.0);  #ifdef DEBUG
       po[i][j][0]=(i==j ? 1.0 : 0.0);      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);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   for(h=1; h <=nhstepm; h++){  #endif
     for(d=1; d <=hstepm; d++){      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       newm=savm;        *xmin=x; 
       /* Covariates have to be included here again */        return fx; 
       cov[1]=1.;      } 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      ftemp=fu;
       if (cptcovn>0){      if (fabs(e) > tol1) { 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];        r=(x-w)*(fx-fv); 
     }        q=(x-v)*(fx-fw); 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        p=(x-v)*q-(x-w)*r; 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        q=2.0*(q-r); 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        if (q > 0.0) p = -p; 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        q=fabs(q); 
       savm=oldm;        etemp=e; 
       oldm=newm;        e=d; 
     }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     for(i=1; i<=nlstate+ndeath; i++)          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for(j=1;j<=nlstate+ndeath;j++) {        else { 
         po[i][j][h]=newm[i][j];          d=p/q; 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);          u=x+d; 
          */          if (u-a < tol2 || b-u < tol2) 
       }            d=SIGN(tol1,xm-x); 
   } /* end h */        } 
   return po;      } else { 
 }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 /*************** log-likelihood *************/      fu=(*f)(u); 
 double func( double *x)      if (fu <= fx) { 
 {        if (u >= x) a=x; else b=x; 
   int i, ii, j, k, mi, d;        SHFT(v,w,x,u) 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];          SHFT(fv,fw,fx,fu) 
   double **out;          } else { 
   double sw; /* Sum of weights */            if (u < x) a=u; else b=u; 
   double lli; /* Individual log likelihood */            if (fu <= fw || w == x) { 
   long ipmx;              v=w; 
   /*extern weight */              w=u; 
   /* We are differentiating ll according to initial status */              fv=fw; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/              fw=fu; 
   /*for(i=1;i<imx;i++)            } else if (fu <= fv || v == x || v == w) { 
 printf(" %d\n",s[4][i]);              v=u; 
   */              fv=fu; 
             } 
   for(k=1; k<=nlstate; k++) ll[k]=0.;          } 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    } 
        for(mi=1; mi<= wav[i]-1; mi++){    nrerror("Too many iterations in brent"); 
       for (ii=1;ii<=nlstate+ndeath;ii++)    *xmin=x; 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    return fx; 
             for(d=0; d<dh[mi][i]; d++){  } 
         newm=savm;  
           cov[1]=1.;  /****************** mnbrak ***********************/
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
           if (cptcovn>0){  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
             for (k=1; k<=cptcovn;k++) cov[2+k]=covar[1+k-1][i];              double (*func)(double)) 
             }  { 
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    double ulim,u,r,q, dum;
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    double fu; 
           savm=oldm;   
           oldm=newm;    *fa=(*func)(*ax); 
     *fb=(*func)(*bx); 
     if (*fb > *fa) { 
       } /* end mult */      SHFT(dum,*ax,*bx,dum) 
            SHFT(dum,*fb,*fa,dum) 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        } 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    *cx=(*bx)+GOLD*(*bx-*ax); 
       ipmx +=1;    *fc=(*func)(*cx); 
       sw += weight[i];    while (*fb > *fc) { 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      r=(*bx-*ax)*(*fb-*fc); 
     } /* end of wave */      q=(*bx-*cx)*(*fb-*fa); 
   } /* end of individual */      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      if ((*bx-u)*(u-*cx) > 0.0) { 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        fu=(*func)(u); 
   return -l;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
 }        fu=(*func)(u); 
         if (fu < *fc) { 
           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
 /*********** Maximum Likelihood Estimation ***************/            SHFT(*fb,*fc,fu,(*func)(u)) 
             } 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
 {        u=ulim; 
   int i,j, iter;        fu=(*func)(u); 
   double **xi,*delti;      } else { 
   double fret;        u=(*cx)+GOLD*(*cx-*bx); 
   xi=matrix(1,npar,1,npar);        fu=(*func)(u); 
   for (i=1;i<=npar;i++)      } 
     for (j=1;j<=npar;j++)      SHFT(*ax,*bx,*cx,u) 
       xi[i][j]=(i==j ? 1.0 : 0.0);        SHFT(*fa,*fb,*fc,fu) 
   printf("Powell\n");        } 
   powell(p,xi,npar,ftol,&iter,&fret,func);  } 
   
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  /*************** linmin ************************/
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));  
   int ncom; 
 }  double *pcom,*xicom;
   double (*nrfunc)(double []); 
 /**** Computes Hessian and covariance matrix ***/   
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
 {  { 
   double  **a,**y,*x,pd;    double brent(double ax, double bx, double cx, 
   double **hess;                 double (*f)(double), double tol, double *xmin); 
   int i, j,jk;    double f1dim(double x); 
   int *indx;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
   double hessii(double p[], double delta, int theta, double delti[]);    int j; 
   double hessij(double p[], double delti[], int i, int j);    double xx,xmin,bx,ax; 
   void lubksb(double **a, int npar, int *indx, double b[]) ;    double fx,fb,fa;
   void ludcmp(double **a, int npar, int *indx, double *d) ;   
     ncom=n; 
     pcom=vector(1,n); 
   hess=matrix(1,npar,1,npar);    xicom=vector(1,n); 
     nrfunc=func; 
   printf("\nCalculation of the hessian matrix. Wait...\n");    for (j=1;j<=n;j++) { 
   for (i=1;i<=npar;i++){      pcom[j]=p[j]; 
     printf("%d",i);fflush(stdout);      xicom[j]=xi[j]; 
     hess[i][i]=hessii(p,ftolhess,i,delti);    } 
     /*printf(" %f ",p[i]);*/    ax=0.0; 
   }    xx=1.0; 
     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   for (i=1;i<=npar;i++) {    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     for (j=1;j<=npar;j++)  {  #ifdef DEBUG
       if (j>i) {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         printf(".%d%d",i,j);fflush(stdout);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         hess[i][j]=hessij(p,delti,i,j);  #endif
         hess[j][i]=hess[i][j];    for (j=1;j<=n;j++) { 
       }      xi[j] *= xmin; 
     }      p[j] += xi[j]; 
   }    } 
   printf("\n");    free_vector(xicom,1,n); 
     free_vector(pcom,1,n); 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  } 
    
   a=matrix(1,npar,1,npar);  char *asc_diff_time(long time_sec, char ascdiff[])
   y=matrix(1,npar,1,npar);  {
   x=vector(1,npar);    long sec_left, days, hours, minutes;
   indx=ivector(1,npar);    days = (time_sec) / (60*60*24);
   for (i=1;i<=npar;i++)    sec_left = (time_sec) % (60*60*24);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    hours = (sec_left) / (60*60) ;
   ludcmp(a,npar,indx,&pd);    sec_left = (sec_left) %(60*60);
     minutes = (sec_left) /60;
   for (j=1;j<=npar;j++) {    sec_left = (sec_left) % (60);
     for (i=1;i<=npar;i++) x[i]=0;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     x[j]=1;    return ascdiff;
     lubksb(a,npar,indx,x);  }
     for (i=1;i<=npar;i++){  
       matcov[i][j]=x[i];  /*************** powell ************************/
     }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   }              double (*func)(double [])) 
   { 
   printf("\n#Hessian matrix#\n");    void linmin(double p[], double xi[], int n, double *fret, 
   for (i=1;i<=npar;i++) {                double (*func)(double [])); 
     for (j=1;j<=npar;j++) {    int i,ibig,j; 
       printf("%.3e ",hess[i][j]);    double del,t,*pt,*ptt,*xit;
     }    double fp,fptt;
     printf("\n");    double *xits;
   }    int niterf, itmp;
   
   /* Recompute Inverse */    pt=vector(1,n); 
   for (i=1;i<=npar;i++)    ptt=vector(1,n); 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    xit=vector(1,n); 
   ludcmp(a,npar,indx,&pd);    xits=vector(1,n); 
     *fret=(*func)(p); 
   /*  printf("\n#Hessian matrix recomputed#\n");    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
   for (j=1;j<=npar;j++) {      fp=(*fret); 
     for (i=1;i<=npar;i++) x[i]=0;      ibig=0; 
     x[j]=1;      del=0.0; 
     lubksb(a,npar,indx,x);      last_time=curr_time;
     for (i=1;i<=npar;i++){      (void) gettimeofday(&curr_time,&tzp);
       y[i][j]=x[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);
       printf("%.3e ",y[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);
     }      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
     printf("\n");      */
   }     for (i=1;i<=n;i++) {
   */        printf(" %d %.12f",i, p[i]);
         fprintf(ficlog," %d %.12lf",i, p[i]);
   free_matrix(a,1,npar,1,npar);        fprintf(ficrespow," %.12lf", p[i]);
   free_matrix(y,1,npar,1,npar);      }
   free_vector(x,1,npar);      printf("\n");
   free_ivector(indx,1,npar);      fprintf(ficlog,"\n");
   free_matrix(hess,1,npar,1,npar);      fprintf(ficrespow,"\n");fflush(ficrespow);
       if(*iter <=3){
         tm = *localtime(&curr_time.tv_sec);
 }        strcpy(strcurr,asctime(&tm));
   /*       asctime_r(&tm,strcurr); */
 /*************** hessian matrix ****************/        forecast_time=curr_time; 
 double hessii( double x[], double delta, int theta, double delti[])        itmp = strlen(strcurr);
 {        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   int i;          strcurr[itmp-1]='\0';
   int l=1, lmax=20;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   double k1,k2;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   double p2[NPARMAX+1];        for(niterf=10;niterf<=30;niterf+=10){
   double res;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          tmf = *localtime(&forecast_time.tv_sec);
   double fx;  /*      asctime_r(&tmf,strfor); */
   int k=0,kmax=10;          strcpy(strfor,asctime(&tmf));
   double l1;          itmp = strlen(strfor);
           if(strfor[itmp-1]=='\n')
   fx=func(x);          strfor[itmp-1]='\0';
   for (i=1;i<=npar;i++) p2[i]=x[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);
   for(l=0 ; l <=lmax; l++){          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);
     l1=pow(10,l);        }
     delts=delt;      }
     for(k=1 ; k <kmax; k=k+1){      for (i=1;i<=n;i++) { 
       delt = delta*(l1*k);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       p2[theta]=x[theta] +delt;        fptt=(*fret); 
       k1=func(p2)-fx;  #ifdef DEBUG
       p2[theta]=x[theta]-delt;        printf("fret=%lf \n",*fret);
       k2=func(p2)-fx;        fprintf(ficlog,"fret=%lf \n",*fret);
       /*res= (k1-2.0*fx+k2)/delt/delt; */  #endif
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        printf("%d",i);fflush(stdout);
              fprintf(ficlog,"%d",i);fflush(ficlog);
 #ifdef DEBUG        linmin(p,xit,n,fret,func); 
       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);        if (fabs(fptt-(*fret)) > del) { 
 #endif          del=fabs(fptt-(*fret)); 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          ibig=i; 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        } 
         k=kmax;  #ifdef DEBUG
       }        printf("%d %.12e",i,(*fret));
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        fprintf(ficlog,"%d %.12e",i,(*fret));
         k=kmax; l=lmax*10.;        for (j=1;j<=n;j++) {
       }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          printf(" x(%d)=%.12e",j,xit[j]);
         delts=delt;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       }        }
     }        for(j=1;j<=n;j++) {
   }          printf(" p=%.12e",p[j]);
   delti[theta]=delts;          fprintf(ficlog," p=%.12e",p[j]);
   return res;        }
          printf("\n");
 }        fprintf(ficlog,"\n");
   #endif
 double hessij( double x[], double delti[], int thetai,int thetaj)      } 
 {      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   int i;  #ifdef DEBUG
   int l=1, l1, lmax=20;        int k[2],l;
   double k1,k2,k3,k4,res,fx;        k[0]=1;
   double p2[NPARMAX+1];        k[1]=-1;
   int k;        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
   fx=func(x);        for (j=1;j<=n;j++) {
   for (k=1; k<=2; k++) {          printf(" %.12e",p[j]);
     for (i=1;i<=npar;i++) p2[i]=x[i];          fprintf(ficlog," %.12e",p[j]);
     p2[thetai]=x[thetai]+delti[thetai]/k;        }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        printf("\n");
     k1=func(p2)-fx;        fprintf(ficlog,"\n");
          for(l=0;l<=1;l++) {
     p2[thetai]=x[thetai]+delti[thetai]/k;          for (j=1;j<=n;j++) {
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     k2=func(p2)-fx;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
              fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     p2[thetai]=x[thetai]-delti[thetai]/k;          }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     k3=func(p2)-fx;          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;  #endif
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k4=func(p2)-fx;  
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        free_vector(xit,1,n); 
 #ifdef DEBUG        free_vector(xits,1,n); 
     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);        free_vector(ptt,1,n); 
 #endif        free_vector(pt,1,n); 
   }        return; 
   return res;      } 
 }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
 /************** Inverse of matrix **************/        ptt[j]=2.0*p[j]-pt[j]; 
 void ludcmp(double **a, int n, int *indx, double *d)        xit[j]=p[j]-pt[j]; 
 {        pt[j]=p[j]; 
   int i,imax,j,k;      } 
   double big,dum,sum,temp;      fptt=(*func)(ptt); 
   double *vv;      if (fptt < fp) { 
          t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   vv=vector(1,n);        if (t < 0.0) { 
   *d=1.0;          linmin(p,xit,n,fret,func); 
   for (i=1;i<=n;i++) {          for (j=1;j<=n;j++) { 
     big=0.0;            xi[j][ibig]=xi[j][n]; 
     for (j=1;j<=n;j++)            xi[j][n]=xit[j]; 
       if ((temp=fabs(a[i][j])) > big) big=temp;          }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  #ifdef DEBUG
     vv[i]=1.0/big;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   }          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   for (j=1;j<=n;j++) {          for(j=1;j<=n;j++){
     for (i=1;i<j;i++) {            printf(" %.12e",xit[j]);
       sum=a[i][j];            fprintf(ficlog," %.12e",xit[j]);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          }
       a[i][j]=sum;          printf("\n");
     }          fprintf(ficlog,"\n");
     big=0.0;  #endif
     for (i=j;i<=n;i++) {        }
       sum=a[i][j];      } 
       for (k=1;k<j;k++)    } 
         sum -= a[i][k]*a[k][j];  } 
       a[i][j]=sum;  
       if ( (dum=vv[i]*fabs(sum)) >= big) {  /**** Prevalence limit (stable prevalence)  ****************/
         big=dum;  
         imax=i;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       }  {
     }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     if (j != imax) {       matrix by transitions matrix until convergence is reached */
       for (k=1;k<=n;k++) {  
         dum=a[imax][k];    int i, ii,j,k;
         a[imax][k]=a[j][k];    double min, max, maxmin, maxmax,sumnew=0.;
         a[j][k]=dum;    double **matprod2();
       }    double **out, cov[NCOVMAX], **pmij();
       *d = -(*d);    double **newm;
       vv[imax]=vv[j];    double agefin, delaymax=50 ; /* Max number of years to converge */
     }  
     indx[j]=imax;    for (ii=1;ii<=nlstate+ndeath;ii++)
     if (a[j][j] == 0.0) a[j][j]=TINY;      for (j=1;j<=nlstate+ndeath;j++){
     if (j != n) {        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       dum=1.0/(a[j][j]);      }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }     cov[1]=1.;
   }   
   free_vector(vv,1,n);  /* Doesn't work */   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 ;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 }      newm=savm;
       /* Covariates have to be included here again */
 void lubksb(double **a, int n, int *indx, double b[])       cov[2]=agefin;
 {    
   int i,ii=0,ip,j;        for (k=1; k<=cptcovn;k++) {
   double sum;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
            /*      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 (i=1;i<=n;i++) {        }
     ip=indx[i];        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     sum=b[ip];        for (k=1; k<=cptcovprod;k++)
     b[ip]=b[i];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     if (ii)  
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     else if (sum) ii=i;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     b[i]=sum;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   }      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   for (i=n;i>=1;i--) {  
     sum=b[i];      savm=oldm;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      oldm=newm;
     b[i]=sum/a[i][i];      maxmax=0.;
   }      for(j=1;j<=nlstate;j++){
 }        min=1.;
         max=0.;
 /************ Frequencies ********************/        for(i=1; i<=nlstate; i++) {
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)          sumnew=0;
 {  /* Some frequencies */          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
            prlim[i][j]= newm[i][j]/(1-sumnew);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          max=FMAX(max,prlim[i][j]);
   double ***freq; /* Frequencies */          min=FMIN(min,prlim[i][j]);
   double *pp;        }
   double pos;        maxmin=max-min;
   FILE *ficresp;        maxmax=FMAX(maxmax,maxmin);
   char fileresp[FILENAMELENGTH];      }
       if(maxmax < ftolpl){
   pp=vector(1,nlstate);        return prlim;
       }
   strcpy(fileresp,"p");    }
   strcat(fileresp,fileres);  }
   if((ficresp=fopen(fileresp,"w"))==NULL) {  
     printf("Problem with prevalence resultfile: %s\n", fileresp);  /*************** transition probabilities ***************/ 
     exit(0);  
   }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  {
   j1=0;    double s1, s2;
     /*double t34;*/
   j=cptcovn;    int i,j,j1, nc, ii, jj;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
       for(i=1; i<= nlstate; i++){
   for(k1=1; k1<=j;k1++){        for(j=1; j<i;j++){
    for(i1=1; i1<=ncodemax[k1];i1++){          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
        j1++;            /*s2 += param[i][j][nc]*cov[nc];*/
             s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         for (i=-1; i<=nlstate+ndeath; i++)    /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
          for (jk=-1; jk<=nlstate+ndeath; jk++)            }
            for(m=agemin; m <= agemax+3; m++)          ps[i][j]=s2;
              freq[i][jk][m]=0;  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
                }
        for (i=1; i<=imx; i++) {        for(j=i+1; j<=nlstate+ndeath;j++){
          bool=1;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
          if  (cptcovn>0) {            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
            for (z1=1; z1<=cptcovn; z1++)  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;          }
          }          ps[i][j]=s2;
           if (bool==1) {        }
            for(m=firstpass; m<=lastpass-1; m++){      }
              if(agev[m][i]==0) agev[m][i]=agemax+1;      /*ps[3][2]=1;*/
              if(agev[m][i]==1) agev[m][i]=agemax+2;      
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      for(i=1; i<= nlstate; i++){
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        s1=0;
            }        for(j=1; j<i; j++)
          }          s1+=exp(ps[i][j]);
        }        for(j=i+1; j<=nlstate+ndeath; j++)
         if  (cptcovn>0) {          s1+=exp(ps[i][j]);
          fprintf(ficresp, "\n#Variable");        ps[i][i]=1./(s1+1.);
          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);        for(j=1; j<i; j++)
        }          ps[i][j]= exp(ps[i][j])*ps[i][i];
        fprintf(ficresp, "\n#");        for(j=i+1; j<=nlstate+ndeath; j++)
        for(i=1; i<=nlstate;i++)          ps[i][j]= exp(ps[i][j])*ps[i][i];
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
        fprintf(ficresp, "\n");      } /* end i */
              
   for(i=(int)agemin; i <= (int)agemax+3; i++){      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     if(i==(int)agemax+3)        for(jj=1; jj<= nlstate+ndeath; jj++){
       printf("Total");          ps[ii][jj]=0;
     else          ps[ii][ii]=1;
       printf("Age %d", i);        }
     for(jk=1; jk <=nlstate ; jk++){      }
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      
         pp[jk] += freq[jk][m][i];  
     }  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
     for(jk=1; jk <=nlstate ; jk++){  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
       for(m=-1, pos=0; m <=0 ; m++)  /*         printf("ddd %lf ",ps[ii][jj]); */
         pos += freq[jk][m][i];  /*       } */
       if(pp[jk]>=1.e-10)  /*       printf("\n "); */
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  /*        } */
       else  /*        printf("\n ");printf("%lf ",cov[2]); */
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);         /*
     }        for(i=1; i<= npar; i++) printf("%f ",x[i]);
     for(jk=1; jk <=nlstate ; jk++){        goto end;*/
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)      return ps;
         pp[jk] += freq[jk][m][i];  }
     }  
     for(jk=1,pos=0; jk <=nlstate ; jk++)  /**************** Product of 2 matrices ******************/
       pos += pp[jk];  
     for(jk=1; jk <=nlstate ; jk++){  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       if(pos>=1.e-5)  {
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       else       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    /* in, b, out are matrice of pointers which should have been initialized 
       if( i <= (int) agemax){       before: only the contents of out is modified. The function returns
         if(pos>=1.e-5)       a pointer to pointers identical to out */
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    long i, j, k;
       else    for(i=nrl; i<= nrh; i++)
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      for(k=ncolol; k<=ncoloh; k++)
       }        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     }          out[i][k] +=in[i][j]*b[j][k];
     for(jk=-1; jk <=nlstate+ndeath; jk++)  
       for(m=-1; m <=nlstate+ndeath; m++)    return out;
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  }
     if(i <= (int) agemax)  
       fprintf(ficresp,"\n");  
     printf("\n");  /************* Higher Matrix Product ***************/
     }  
     }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
  }  {
      /* Computes the transition matrix starting at age 'age' over 
   fclose(ficresp);       'nhstepm*hstepm*stepm' months (i.e. until
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   free_vector(pp,1,nlstate);       nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
 }  /* End of Freq */       (typically every 2 years instead of every month which is too big 
        for the memory).
 /************* Waves Concatenation ***************/       Model is determined by parameters x and covariates have to be 
        included manually here. 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  
 {       */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  
      Death is a valid wave (if date is known).    int i, j, d, h, k;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    double **out, cov[NCOVMAX];
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    double **newm;
      and mw[mi+1][i]. dh depends on stepm.  
      */    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
   int i, mi, m;      for (j=1;j<=nlstate+ndeath;j++){
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        oldm[i][j]=(i==j ? 1.0 : 0.0);
 float sum=0.;        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
   for(i=1; i<=imx; i++){    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     mi=0;    for(h=1; h <=nhstepm; h++){
     m=firstpass;      for(d=1; d <=hstepm; d++){
     while(s[m][i] <= nlstate){        newm=savm;
       if(s[m][i]>=1)        /* Covariates have to be included here again */
         mw[++mi][i]=m;        cov[1]=1.;
       if(m >=lastpass)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         break;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       else        for (k=1; k<=cptcovage;k++)
         m++;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     }/* end while */        for (k=1; k<=cptcovprod;k++)
     if (s[m][i] > nlstate){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       mi++;     /* Death is another wave */  
       /* if(mi==0)  never been interviewed correctly before death */  
          /* Only death is a correct wave */        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       mw[mi][i]=m;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     }        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
     wav[i]=mi;        savm=oldm;
     if(mi==0)        oldm=newm;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      }
   }      for(i=1; i<=nlstate+ndeath; i++)
         for(j=1;j<=nlstate+ndeath;j++) {
   for(i=1; i<=imx; i++){          po[i][j][h]=newm[i][j];
     for(mi=1; mi<wav[i];mi++){          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       if (stepm <=0)           */
         dh[mi][i]=1;        }
       else{    } /* end h */
         if (s[mw[mi+1][i]][i] > nlstate) {    return po;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  }
           if(j=0) j=1;  /* Survives at least one month after exam */  
         }  
         else{  /*************** log-likelihood *************/
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  double func( double *x)
           k=k+1;  {
           if (j >= jmax) jmax=j;    int i, ii, j, k, mi, d, kk;
           else if (j <= jmin)jmin=j;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
           sum=sum+j;    double **out;
         }    double sw; /* Sum of weights */
         jk= j/stepm;    double lli; /* Individual log likelihood */
         jl= j -jk*stepm;    int s1, s2;
         ju= j -(jk+1)*stepm;    double bbh, survp;
         if(jl <= -ju)    long ipmx;
           dh[mi][i]=jk;    /*extern weight */
         else    /* We are differentiating ll according to initial status */
           dh[mi][i]=jk+1;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         if(dh[mi][i]==0)    /*for(i=1;i<imx;i++) 
           dh[mi][i]=1; /* At least one step */      printf(" %d\n",s[4][i]);
       }    */
     }    cov[1]=1.;
   }  
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);    for(k=1; k<=nlstate; k++) ll[k]=0.;
 }  
 /*********** Tricode ****************************/    if(mle==1){
 void tricode(int *Tvar, int **nbcode, int imx)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int Ndum[80],ij, k, j, i;        for(mi=1; mi<= wav[i]-1; mi++){
   int cptcode=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
   for (k=0; k<79; k++) Ndum[k]=0;            for (j=1;j<=nlstate+ndeath;j++){
   for (k=1; k<=7; k++) ncodemax[k]=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (j=1; j<=cptcovn; j++) {            }
     for (i=1; i<=imx; i++) {          for(d=0; d<dh[mi][i]; d++){
       ij=(int)(covar[Tvar[j]][i]);            newm=savm;
       Ndum[ij]++;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if (ij > cptcode) cptcode=ij;            for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/            }
     for (i=0; i<=cptcode; i++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       if(Ndum[i]!=0) ncodemax[j]++;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
              oldm=newm;
     ij=1;          } /* end mult */
     for (i=1; i<=ncodemax[j]; i++) {        
       for (k=0; k<=79; k++) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         if (Ndum[k] != 0) {          /* But now since version 0.9 we anticipate for bias at large stepm.
           nbcode[Tvar[j]][ij]=k;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
           ij++;           * (in months) between two waves is not a multiple of stepm, we rounded to 
         }           * the nearest (and in case of equal distance, to the lowest) interval but now
         if (ij > ncodemax[j]) break;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       }             * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
     }           * probability in order to take into account the bias as a fraction of the way
   }             * from savm to out if bh is negative or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
   }           * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
 /*********** Health Expectancies ****************/           */
           s1=s[mw[mi][i]][i];
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          s2=s[mw[mi+1][i]][i];
 {          bbh=(double)bh[mi][i]/(double)stepm; 
   /* Health expectancies */          /* bias bh is positive if real duration
   int i, j, nhstepm, hstepm, h;           * is higher than the multiple of stepm and negative otherwise.
   double age, agelim,hf;           */
   double ***p3mat;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
            if( s2 > nlstate){ 
   fprintf(ficreseij,"# Health expectancies\n");            /* i.e. if s2 is a death state and if the date of death is known 
   fprintf(ficreseij,"# Age");               then the contribution to the likelihood is the probability to 
   for(i=1; i<=nlstate;i++)               die between last step unit time and current  step unit time, 
     for(j=1; j<=nlstate;j++)               which is also equal to probability to die before dh 
       fprintf(ficreseij," %1d-%1d",i,j);               minus probability to die before dh-stepm . 
   fprintf(ficreseij,"\n");               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
   hstepm=1*YEARM; /*  Every j years of age (in month) */          health state: the date of the interview describes the actual state
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          and not the date of a change in health state. The former idea was
           to consider that at each interview the state was recorded
   agelim=AGESUP;          (healthy, disable or death) and IMaCh was corrected; but when we
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          introduced the exact date of death then we should have modified
     /* nhstepm age range expressed in number of stepm */          the contribution of an exact death to the likelihood. This new
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);          contribution is smaller and very dependent of the step unit
     /* Typically if 20 years = 20*12/6=40 stepm */          stepm. It is no more the probability to die between last interview
     if (stepm >= YEARM) hstepm=1;          and month of death but the probability to survive from last
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */          interview up to one month before death multiplied by the
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          probability to die within a month. Thanks to Chris
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          Jackson for correcting this bug.  Former versions increased
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          mortality artificially. The bad side is that we add another loop
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            which slows down the processing. The difference can be up to 10%
           lower mortality.
             */
     for(i=1; i<=nlstate;i++)            lli=log(out[s1][s2] - savm[s1][s2]);
       for(j=1; j<=nlstate;j++)  
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){  
           eij[i][j][(int)age] +=p3mat[i][j][h];          } else if  (s2==-2) {
         }            for (j=1,survp=0. ; j<=nlstate; j++) 
                  survp += out[s1][j];
     hf=1;            lli= survp;
     if (stepm >= YEARM) hf=stepm/YEARM;          }
     fprintf(ficreseij,"%.0f",age );          
     for(i=1; i<=nlstate;i++)          else if  (s2==-4) {
       for(j=1; j<=nlstate;j++){            for (j=3,survp=0. ; j<=nlstate; j++) 
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);              survp += out[s1][j];
       }            lli= survp;
     fprintf(ficreseij,"\n");          }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          
   }          else if  (s2==-5) {
 }            for (j=1,survp=0. ; j<=2; j++) 
               survp += out[s1][j];
 /************ Variance ******************/            lli= survp;
 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)          }
 {  
   /* Variance of health expectancies */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          else{
   double **newm;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double **dnewm,**doldm;            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   int i, j, nhstepm, hstepm, h;          } 
   int k, cptcode;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
    double *xp;          /*if(lli ==000.0)*/
   double **gp, **gm;          /*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); */
   double ***gradg, ***trgradg;          ipmx +=1;
   double ***p3mat;          sw += weight[i];
   double age,agelim;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int theta;        } /* end of wave */
       } /* end of individual */
    fprintf(ficresvij,"# Covariances of life expectancies\n");    }  else if(mle==2){
   fprintf(ficresvij,"# Age");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for(i=1; i<=nlstate;i++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for(j=1; j<=nlstate;j++)        for(mi=1; mi<= wav[i]-1; mi++){
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          for (ii=1;ii<=nlstate+ndeath;ii++)
   fprintf(ficresvij,"\n");            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   xp=vector(1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   dnewm=matrix(1,nlstate,1,npar);            }
   doldm=matrix(1,nlstate,1,nlstate);          for(d=0; d<=dh[mi][i]; d++){
              newm=savm;
   hstepm=1*YEARM; /* Every year of age */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            for (kk=1; kk<=cptcovage;kk++) {
   agelim = AGESUP;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     if (stepm >= YEARM) hstepm=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            savm=oldm;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            oldm=newm;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          } /* end mult */
     gp=matrix(0,nhstepm,1,nlstate);        
     gm=matrix(0,nhstepm,1,nlstate);          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
     for(theta=1; theta <=npar; theta++){          bbh=(double)bh[mi][i]/(double)stepm; 
       for(i=1; i<=npar; i++){ /* Computes gradient */          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 */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          ipmx +=1;
       }          sw += weight[i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        } /* end of wave */
       for(j=1; j<= nlstate; j++){      } /* end of individual */
         for(h=0; h<=nhstepm; h++){    }  else if(mle==3){  /* exponential inter-extrapolation */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
                for (j=1;j<=nlstate+ndeath;j++){
       for(i=1; i<=npar; i++) /* Computes gradient */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         xp[i] = x[i] - (i==theta ?delti[theta]: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, gm[h][j]=0.;i<=nlstate;i++)            for (kk=1; kk<=cptcovage;kk++) {
             gm[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,
       for(j=1; j<= nlstate; j++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         for(h=0; h<=nhstepm; h++){            savm=oldm;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            oldm=newm;
         }          } /* end mult */
     } /* End theta */        
           s1=s[mw[mi][i]][i];
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
     for(h=0; h<=nhstepm; 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 */
       for(j=1; j<=nlstate;j++)          ipmx +=1;
         for(theta=1; theta <=npar; theta++)          sw += weight[i];
           trgradg[h][j][theta]=gradg[h][theta][j];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
     for(i=1;i<=nlstate;i++)      } /* end of individual */
       for(j=1;j<=nlstate;j++)    }else if (mle==4){  /* ml=4 no inter-extrapolation */
         vareij[i][j][(int)age] =0.;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(h=0;h<=nhstepm;h++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(k=0;k<=nhstepm;k++){        for(mi=1; mi<= wav[i]-1; mi++){
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          for (ii=1;ii<=nlstate+ndeath;ii++)
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            for (j=1;j<=nlstate+ndeath;j++){
         for(i=1;i<=nlstate;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(j=1;j<=nlstate;j++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             vareij[i][j][(int)age] += doldm[i][j];            }
       }          for(d=0; d<dh[mi][i]; d++){
     }            newm=savm;
     h=1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     if (stepm >= YEARM) h=stepm/YEARM;            for (kk=1; kk<=cptcovage;kk++) {
     fprintf(ficresvij,"%.0f ",age );              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(i=1; i<=nlstate;i++)            }
       for(j=1; j<=nlstate;j++){          
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     fprintf(ficresvij,"\n");            savm=oldm;
     free_matrix(gp,0,nhstepm,1,nlstate);            oldm=newm;
     free_matrix(gm,0,nhstepm,1,nlstate);          } /* end mult */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          s1=s[mw[mi][i]][i];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          s2=s[mw[mi+1][i]][i];
   } /* End age */          if( s2 > nlstate){ 
              lli=log(out[s1][s2] - savm[s1][s2]);
   free_vector(xp,1,npar);          }else{
   free_matrix(doldm,1,nlstate,1,npar);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   free_matrix(dnewm,1,nlstate,1,nlstate);          }
           ipmx +=1;
 }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /************ Variance of prevlim ******************/  /*      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]); */
 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)        } /* end of wave */
 {      } /* end of individual */
   /* Variance of prevalence limit */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double **newm;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double **dnewm,**doldm;        for(mi=1; mi<= wav[i]-1; mi++){
   int i, j, nhstepm, hstepm;          for (ii=1;ii<=nlstate+ndeath;ii++)
   int k, cptcode;            for (j=1;j<=nlstate+ndeath;j++){
   double *xp;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double *gp, *gm;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **gradg, **trgradg;            }
   double age,agelim;          for(d=0; d<dh[mi][i]; d++){
   int theta;            newm=savm;
                cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");            for (kk=1; kk<=cptcovage;kk++) {
   fprintf(ficresvpl,"# Age");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for(i=1; i<=nlstate;i++)            }
       fprintf(ficresvpl," %1d-%1d",i,i);          
   fprintf(ficresvpl,"\n");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   xp=vector(1,npar);            savm=oldm;
   dnewm=matrix(1,nlstate,1,npar);            oldm=newm;
   doldm=matrix(1,nlstate,1,nlstate);          } /* end mult */
          
   hstepm=1*YEARM; /* Every year of age */          s1=s[mw[mi][i]][i];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          s2=s[mw[mi+1][i]][i];
   agelim = AGESUP;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   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 */          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
     gradg=matrix(1,npar,1,nlstate);        } /* end of wave */
     gp=vector(1,nlstate);      } /* end of individual */
     gm=vector(1,nlstate);    } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     for(theta=1; theta <=npar; theta++){    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       for(i=1; i<=npar; i++){ /* Computes gradient */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    return -l;
       }  }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)  /*************** log-likelihood *************/
         gp[i] = prlim[i][i];  double funcone( double *x)
      {
       for(i=1; i<=npar; i++) /* Computes gradient */    /* Same as likeli but slower because of a lot of printf and if */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    int i, ii, j, k, mi, d, kk;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       for(i=1;i<=nlstate;i++)    double **out;
         gm[i] = prlim[i][i];    double lli; /* Individual log likelihood */
     double llt;
       for(i=1;i<=nlstate;i++)    int s1, s2;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    double bbh, survp;
     } /* End theta */    /*extern weight */
     /* We are differentiating ll according to initial status */
     trgradg =matrix(1,nlstate,1,npar);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
     for(j=1; j<=nlstate;j++)      printf(" %d\n",s[4][i]);
       for(theta=1; theta <=npar; theta++)    */
         trgradg[j][theta]=gradg[theta][j];    cov[1]=1.;
   
     for(i=1;i<=nlstate;i++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
       varpl[i][(int)age] =0.;  
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for(i=1;i<=nlstate;i++)      for(mi=1; mi<= wav[i]-1; mi++){
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
     fprintf(ficresvpl,"%.0f ",age );            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i=1; i<=nlstate;i++)            savm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          }
     fprintf(ficresvpl,"\n");        for(d=0; d<dh[mi][i]; d++){
     free_vector(gp,1,nlstate);          newm=savm;
     free_vector(gm,1,nlstate);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     free_matrix(gradg,1,npar,1,nlstate);          for (kk=1; kk<=cptcovage;kk++) {
     free_matrix(trgradg,1,nlstate,1,npar);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   } /* End age */          }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   free_vector(xp,1,npar);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_matrix(doldm,1,nlstate,1,npar);          savm=oldm;
   free_matrix(dnewm,1,nlstate,1,nlstate);          oldm=newm;
         } /* end mult */
 }        
         s1=s[mw[mi][i]][i];
         s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm; 
 /***********************************************/        /* bias is positive if real duration
 /**************** Main Program *****************/         * is higher than the multiple of stepm and negative otherwise.
 /***********************************************/         */
         if( s2 > nlstate && (mle <5) ){  /* Jackson */
 /*int main(int argc, char *argv[])*/          lli=log(out[s1][s2] - savm[s1][s2]);
 int main()        } else if (mle==1){
 {          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;          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 */
   double agedeb, agefin,hf;        } else if(mle==3){  /* exponential inter-extrapolation */
   double agemin=1.e20, agemax=-1.e20;          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 */
   double fret;          lli=log(out[s1][s2]); /* Original formula */
   double **xi,tmp,delta;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           lli=log(out[s1][s2]); /* Original formula */
   double dum; /* Dummy variable */        } /* End of if */
   double ***p3mat;        ipmx +=1;
   int *indx;        sw += weight[i];
   char line[MAXLINE], linepar[MAXLINE];        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   char title[MAXLINE];  /*       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]); */
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];        if(globpr){
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
   char filerest[FILENAMELENGTH];   %10.6f %10.6f %10.6f ", \
   char fileregp[FILENAMELENGTH];                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   int firstobs=1, lastobs=10;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   int sdeb, sfin; /* Status at beginning and end */            llt +=ll[k]*gipmx/gsw;
   int c,  h , cpt,l;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   int ju,jl, mi;          }
   int i1,j1, k1,jk,aa,bb, stepsize;          fprintf(ficresilk," %10.6f\n", -llt);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        }
        } /* end of wave */
   int hstepm, nhstepm;    } /* end of individual */
   double bage, fage, age, agelim, agebase;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   double ftolpl=FTOL;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   double **prlim;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   double *severity;    if(globpr==0){ /* First time we count the contributions and weights */
   double ***param; /* Matrix of parameters */      gipmx=ipmx;
   double  *p;      gsw=sw;
   double **matcov; /* Matrix of covariance */    }
   double ***delti3; /* Scale */    return -l;
   double *delti; /* Scale */  }
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;  /*************** function likelione ***********/
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   char *alph[]={"a","a","b","c","d","e"}, str[4];  {
   char z[1]="c", occ;    /* This routine should help understanding what is done with 
 #include <sys/time.h>       the selection of individuals/waves and
 #include <time.h>       to check the exact contribution to the likelihood.
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];       Plotting could be done.
   /* long total_usecs;     */
   struct timeval start_time, end_time;    int k;
    
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
       strcat(fileresilk,fileres);
   printf("\nIMACH, Version 0.63");      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   printf("\nEnter the parameter file name: ");        printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
 #ifdef windows      }
   scanf("%s",pathtot);      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");
   getcwd(pathcd, size);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   cutv(path,optionfile,pathtot,'\\');      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   chdir(path);      for(k=1; k<=nlstate; k++) 
   replace(pathc,path);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
 #endif      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
 #ifdef unix    }
   scanf("%s",optionfile);  
 #endif    *fretone=(*funcone)(p);
     if(*globpri !=0){
 /*-------- arguments in the command line --------*/      fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   strcpy(fileres,"r");      fflush(fichtm); 
   strcat(fileres, optionfile);    } 
     return;
   /*---------arguments file --------*/  }
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  
     printf("Problem with optionfile %s\n",optionfile);  /*********** Maximum Likelihood Estimation ***************/
     goto end;  
   }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
   strcpy(filereso,"o");    int i,j, iter;
   strcat(filereso,fileres);    double **xi;
   if((ficparo=fopen(filereso,"w"))==NULL) {    double fret;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    double fretone; /* Only one call to likelihood */
   }    /*  char filerespow[FILENAMELENGTH];*/
     xi=matrix(1,npar,1,npar);
   /* Reads comments: lines beginning with '#' */    for (i=1;i<=npar;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){      for (j=1;j<=npar;j++)
     ungetc(c,ficpar);        xi[i][j]=(i==j ? 1.0 : 0.0);
     fgets(line, MAXLINE, ficpar);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     puts(line);    strcpy(filerespow,"pow"); 
     fputs(line,ficparo);    strcat(filerespow,fileres);
   }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   ungetc(c,ficpar);      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    }
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
   covar=matrix(1,NCOVMAX,1,n);            if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   if (strlen(model)<=1) cptcovn=0;    fprintf(ficrespow,"\n");
   else {  
     j=0;    powell(p,xi,npar,ftol,&iter,&fret,func);
     j=nbocc(model,'+');  
     cptcovn=j+1;    fclose(ficrespow);
   }    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   ncovmodel=2+cptcovn;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
    }
   /* Read guess parameters */  
   /* Reads comments: lines beginning with '#' */  /**** Computes Hessian and covariance matrix ***/
   while((c=getc(ficpar))=='#' && c!= EOF){  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     ungetc(c,ficpar);  {
     fgets(line, MAXLINE, ficpar);    double  **a,**y,*x,pd;
     puts(line);    double **hess;
     fputs(line,ficparo);    int i, j,jk;
   }    int *indx;
   ungetc(c,ficpar);  
      double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     for(i=1; i <=nlstate; i++)    void lubksb(double **a, int npar, int *indx, double b[]) ;
     for(j=1; j <=nlstate+ndeath-1; j++){    void ludcmp(double **a, int npar, int *indx, double *d) ;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    double gompertz(double p[]);
       fprintf(ficparo,"%1d%1d",i1,j1);    hess=matrix(1,npar,1,npar);
       printf("%1d%1d",i,j);  
       for(k=1; k<=ncovmodel;k++){    printf("\nCalculation of the hessian matrix. Wait...\n");
         fscanf(ficpar," %lf",&param[i][j][k]);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         printf(" %lf",param[i][j][k]);    for (i=1;i<=npar;i++){
         fprintf(ficparo," %lf",param[i][j][k]);      printf("%d",i);fflush(stdout);
       }      fprintf(ficlog,"%d",i);fflush(ficlog);
       fscanf(ficpar,"\n");     
       printf("\n");       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       fprintf(ficparo,"\n");      
     }      /*  printf(" %f ",p[i]);
            printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    }
   p=param[1][1];    
      for (i=1;i<=npar;i++) {
   /* Reads comments: lines beginning with '#' */      for (j=1;j<=npar;j++)  {
   while((c=getc(ficpar))=='#' && c!= EOF){        if (j>i) { 
     ungetc(c,ficpar);          printf(".%d%d",i,j);fflush(stdout);
     fgets(line, MAXLINE, ficpar);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     puts(line);          hess[i][j]=hessij(p,delti,i,j,func,npar);
     fputs(line,ficparo);          
   }          hess[j][i]=hess[i][j];    
   ungetc(c,ficpar);          /*printf(" %lf ",hess[i][j]);*/
         }
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      }
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    }
   for(i=1; i <=nlstate; i++){    printf("\n");
     for(j=1; j <=nlstate+ndeath-1; j++){    fprintf(ficlog,"\n");
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       fprintf(ficparo,"%1d%1d",i1,j1);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       for(k=1; k<=ncovmodel;k++){    
         fscanf(ficpar,"%le",&delti3[i][j][k]);    a=matrix(1,npar,1,npar);
         printf(" %le",delti3[i][j][k]);    y=matrix(1,npar,1,npar);
         fprintf(ficparo," %le",delti3[i][j][k]);    x=vector(1,npar);
       }    indx=ivector(1,npar);
       fscanf(ficpar,"\n");    for (i=1;i<=npar;i++)
       printf("\n");      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       fprintf(ficparo,"\n");    ludcmp(a,npar,indx,&pd);
     }  
   }    for (j=1;j<=npar;j++) {
   delti=delti3[1][1];      for (i=1;i<=npar;i++) x[i]=0;
        x[j]=1;
   /* Reads comments: lines beginning with '#' */      lubksb(a,npar,indx,x);
   while((c=getc(ficpar))=='#' && c!= EOF){      for (i=1;i<=npar;i++){ 
     ungetc(c,ficpar);        matcov[i][j]=x[i];
     fgets(line, MAXLINE, ficpar);      }
     puts(line);    }
     fputs(line,ficparo);  
   }    printf("\n#Hessian matrix#\n");
   ungetc(c,ficpar);    fprintf(ficlog,"\n#Hessian matrix#\n");
      for (i=1;i<=npar;i++) { 
   matcov=matrix(1,npar,1,npar);      for (j=1;j<=npar;j++) { 
   for(i=1; i <=npar; i++){        printf("%.3e ",hess[i][j]);
     fscanf(ficpar,"%s",&str);        fprintf(ficlog,"%.3e ",hess[i][j]);
     printf("%s",str);      }
     fprintf(ficparo,"%s",str);      printf("\n");
     for(j=1; j <=i; j++){      fprintf(ficlog,"\n");
       fscanf(ficpar," %le",&matcov[i][j]);    }
       printf(" %.5le",matcov[i][j]);  
       fprintf(ficparo," %.5le",matcov[i][j]);    /* Recompute Inverse */
     }    for (i=1;i<=npar;i++)
     fscanf(ficpar,"\n");      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     printf("\n");    ludcmp(a,npar,indx,&pd);
     fprintf(ficparo,"\n");  
   }    /*  printf("\n#Hessian matrix recomputed#\n");
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)    for (j=1;j<=npar;j++) {
       matcov[i][j]=matcov[j][i];      for (i=1;i<=npar;i++) x[i]=0;
          x[j]=1;
   printf("\n");      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
         y[i][j]=x[i];
    if(mle==1){        printf("%.3e ",y[i][j]);
     /*-------- data file ----------*/        fprintf(ficlog,"%.3e ",y[i][j]);
     if((ficres =fopen(fileres,"w"))==NULL) {      }
       printf("Problem with resultfile: %s\n", fileres);goto end;      printf("\n");
     }      fprintf(ficlog,"\n");
     fprintf(ficres,"#%s\n",version);    }
        */
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;    free_matrix(a,1,npar,1,npar);
     }    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
     n= lastobs;    free_ivector(indx,1,npar);
     severity = vector(1,maxwav);    free_matrix(hess,1,npar,1,npar);
     outcome=imatrix(1,maxwav+1,1,n);  
     num=ivector(1,n);  
     moisnais=vector(1,n);  }
     annais=vector(1,n);  
     moisdc=vector(1,n);  /*************** hessian matrix ****************/
     andc=vector(1,n);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     agedc=vector(1,n);  {
     cod=ivector(1,n);    int i;
     weight=vector(1,n);    int l=1, lmax=20;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    double k1,k2;
     mint=matrix(1,maxwav,1,n);    double p2[NPARMAX+1];
     anint=matrix(1,maxwav,1,n);    double res;
     s=imatrix(1,maxwav+1,1,n);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     adl=imatrix(1,maxwav+1,1,n);        double fx;
     tab=ivector(1,NCOVMAX);    int k=0,kmax=10;
     ncodemax=ivector(1,8);    double l1;
   
     i=1;    fx=func(x);
     while (fgets(line, MAXLINE, fic) != NULL)    {    for (i=1;i<=npar;i++) p2[i]=x[i];
       if ((i >= firstobs) && (i <=lastobs)) {    for(l=0 ; l <=lmax; l++){
              l1=pow(10,l);
         for (j=maxwav;j>=1;j--){      delts=delt;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      for(k=1 ; k <kmax; k=k+1){
           strcpy(line,stra);        delt = delta*(l1*k);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        p2[theta]=x[theta] +delt;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        k1=func(p2)-fx;
         }        p2[theta]=x[theta]-delt;
                k2=func(p2)-fx;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        /*res= (k1-2.0*fx+k2)/delt/delt; */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  #ifdef DEBUG
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  #endif
         for (j=ncov;j>=1;j--){        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         }          k=kmax;
         num[i]=atol(stra);        }
         else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         /*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]));*/          k=kmax; l=lmax*10.;
         }
         i=i+1;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       }          delts=delt;
     }        }
       }
     /*scanf("%d",i);*/    }
   imx=i-1; /* Number of individuals */    delti[theta]=delts;
     return res; 
   /* Calculation of the number of parameter from char model*/    
   Tvar=ivector(1,8);      }
      
   if (strlen(model) >1){  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     j=0;  {
     j=nbocc(model,'+');    int i;
     cptcovn=j+1;    int l=1, l1, lmax=20;
        double k1,k2,k3,k4,res,fx;
     strcpy(modelsav,model);    double p2[NPARMAX+1];
     if (j==0) {    int k;
       cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb);  
     }    fx=func(x);
     else {    for (k=1; k<=2; k++) {
       for(i=j; i>=1;i--){      for (i=1;i<=npar;i++) p2[i]=x[i];
         cutv(stra,strb,modelsav,'+');      p2[thetai]=x[thetai]+delti[thetai]/k;
         if (strchr(strb,'*')) {      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           cutv(strd,strc,strb,'*');      k1=func(p2)-fx;
           cutv(strb,stre,strc,'V');Tvar[i+1]=ncov+1;    
           cutv(strb,strc,strd,'V');      p2[thetai]=x[thetai]+delti[thetai]/k;
           for (k=1; k<=lastobs;k++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
             covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      k2=func(p2)-fx;
         }    
         else {cutv(strd,strc,strb,'V');      p2[thetai]=x[thetai]-delti[thetai]/k;
         Tvar[i+1]=atoi(strc);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         }      k3=func(p2)-fx;
         strcpy(modelsav,stra);      
       }      p2[thetai]=x[thetai]-delti[thetai]/k;
       cutv(strd,strc,stra,'V');      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       Tvar[1]=atoi(strc);      k4=func(p2)-fx;
     }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   }  #ifdef DEBUG
   /*printf("tvar=%d ",Tvar[1]);      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);
   scanf("%d ",i);*/      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);
     fclose(fic);  #endif
     }
     if (weightopt != 1) { /* Maximisation without weights*/    return res;
       for(i=1;i<=n;i++) weight[i]=1.0;  }
     }  
     /*-calculation of age at interview from date of interview and age at death -*/  /************** Inverse of matrix **************/
     agev=matrix(1,maxwav,1,imx);  void ludcmp(double **a, int n, int *indx, double *d) 
      { 
     for (i=1; i<=imx; i++)  {    int i,imax,j,k; 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    double big,dum,sum,temp; 
       for(m=1; (m<= maxwav); m++){    double *vv; 
         if(s[m][i] >0){   
           if (s[m][i] == nlstate+1) {    vv=vector(1,n); 
             if(agedc[i]>0)    *d=1.0; 
               if(moisdc[i]!=99 && andc[i]!=9999)    for (i=1;i<=n;i++) { 
               agev[m][i]=agedc[i];      big=0.0; 
             else{      for (j=1;j<=n;j++) 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        if ((temp=fabs(a[i][j])) > big) big=temp; 
               agev[m][i]=-1;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
             }      vv[i]=1.0/big; 
           }    } 
           else if(s[m][i] !=9){ /* Should no more exist */    for (j=1;j<=n;j++) { 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      for (i=1;i<j;i++) { 
             if(mint[m][i]==99 || anint[m][i]==9999)        sum=a[i][j]; 
               agev[m][i]=1;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
             else if(agev[m][i] <agemin){        a[i][j]=sum; 
               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);*/      big=0.0; 
             }      for (i=j;i<=n;i++) { 
             else if(agev[m][i] >agemax){        sum=a[i][j]; 
               agemax=agev[m][i];        for (k=1;k<j;k++) 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/          sum -= a[i][k]*a[k][j]; 
             }        a[i][j]=sum; 
             /*agev[m][i]=anint[m][i]-annais[i];*/        if ( (dum=vv[i]*fabs(sum)) >= big) { 
             /*   agev[m][i] = age[i]+2*m;*/          big=dum; 
           }          imax=i; 
           else { /* =9 */        } 
             agev[m][i]=1;      } 
             s[m][i]=-1;      if (j != imax) { 
           }        for (k=1;k<=n;k++) { 
         }          dum=a[imax][k]; 
         else /*= 0 Unknown */          a[imax][k]=a[j][k]; 
           agev[m][i]=1;          a[j][k]=dum; 
       }        } 
            *d = -(*d); 
     }        vv[imax]=vv[j]; 
     for (i=1; i<=imx; i++)  {      } 
       for(m=1; (m<= maxwav); m++){      indx[j]=imax; 
         if (s[m][i] > (nlstate+ndeath)) {      if (a[j][j] == 0.0) a[j][j]=TINY; 
           printf("Error: Wrong value in nlstate or ndeath\n");        if (j != n) { 
           goto end;        dum=1.0/(a[j][j]); 
         }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       }      } 
     }    } 
     free_vector(vv,1,n);  /* Doesn't work */
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  ;
   } 
     free_vector(severity,1,maxwav);  
     free_imatrix(outcome,1,maxwav+1,1,n);  void lubksb(double **a, int n, int *indx, double b[]) 
     free_vector(moisnais,1,n);  { 
     free_vector(annais,1,n);    int i,ii=0,ip,j; 
     free_matrix(mint,1,maxwav,1,n);    double sum; 
     free_matrix(anint,1,maxwav,1,n);   
     free_vector(moisdc,1,n);    for (i=1;i<=n;i++) { 
     free_vector(andc,1,n);      ip=indx[i]; 
       sum=b[ip]; 
          b[ip]=b[i]; 
     wav=ivector(1,imx);      if (ii) 
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      else if (sum) ii=i; 
          b[i]=sum; 
     /* Concatenates waves */    } 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    for (i=n;i>=1;i--) { 
       sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
 Tcode=ivector(1,100);      b[i]=sum/a[i][i]; 
    nbcode=imatrix(1,nvar,1,8);      } 
    ncodemax[1]=1;  } 
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);  
    /************ Frequencies ********************/
    codtab=imatrix(1,100,1,10);  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[])
    h=0;  {  /* Some frequencies */
    m=pow(2,cptcovn);    
      int i, m, jk, k1,i1, j1, bool, z1,z2,j;
    for(k=1;k<=cptcovn; k++){    int first;
      for(i=1; i <=(m/pow(2,k));i++){    double ***freq; /* Frequencies */
        for(j=1; j <= ncodemax[k]; j++){    double *pp, **prop;
          for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){    double pos,posprop, k2, dateintsum=0,k2cpt=0;
            h++;    FILE *ficresp;
            if (h>m) h=1;codtab[h][k]=j;    char fileresp[FILENAMELENGTH];
          }    
        }    pp=vector(1,nlstate);
      }    prop=matrix(1,nlstate,iagemin,iagemax+3);
    }    strcpy(fileresp,"p");
     strcat(fileresp,fileres);
    /*for(i=1; i <=m ;i++){    if((ficresp=fopen(fileresp,"w"))==NULL) {
      for(k=1; k <=cptcovn; k++){      printf("Problem with prevalence resultfile: %s\n", fileresp);
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
      }      exit(0);
      printf("\n");    }
    }*/    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
    /*scanf("%d",i);*/    j1=0;
        
    /* Calculates basic frequencies. Computes observed prevalence at single age    j=cptcoveff;
        and prints on file fileres'p'. */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);  
     first=1;
   
   /*scanf("%d ",i);*/    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          scanf("%d", i);*/
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for (i=-5; i<=nlstate+ndeath; i++)  
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for (jk=-5; jk<=nlstate+ndeath; jk++)  
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            for(m=iagemin; m <= iagemax+3; m++)
                  freq[i][jk][m]=0;
     /* 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] */      for (i=1; i<=nlstate; i++)  
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        for(m=iagemin; m <= iagemax+3; m++)
              prop[i][m]=0;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        
         dateintsum=0;
            k2cpt=0;
     /*--------- results files --------------*/        for (i=1; i<=imx; i++) {
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);          bool=1;
              if  (cptcovn>0) {
    jk=1;            for (z1=1; z1<=cptcoveff; z1++) 
    fprintf(ficres,"# Parameters\n");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
    printf("# Parameters\n");                bool=0;
    for(i=1,jk=1; i <=nlstate; i++){          }
      for(k=1; k <=(nlstate+ndeath); k++){          if (bool==1){
        if (k != i)            for(m=firstpass; m<=lastpass; m++){
          {              k2=anint[m][i]+(mint[m][i]/12.);
            printf("%d%d ",i,k);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
            fprintf(ficres,"%1d%1d ",i,k);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
            for(j=1; j <=ncovmodel; j++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
              printf("%f ",p[jk]);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
              fprintf(ficres,"%f ",p[jk]);                if (m<lastpass) {
              jk++;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
            }                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
            printf("\n");                }
            fprintf(ficres,"\n");                
          }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
      }                  dateintsum=dateintsum+k2;
    }                  k2cpt++;
                 }
     /* Computing hessian and covariance matrix */                /*}*/
     ftolhess=ftol; /* Usually correct */            }
     hesscov(matcov, p, npar, delti, ftolhess, func);          }
     fprintf(ficres,"# Scales\n");        }
     printf("# Scales\n");         
      for(i=1,jk=1; i <=nlstate; i++){        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       for(j=1; j <=nlstate+ndeath; j++){  fprintf(ficresp, "#Local time at start: %s", strstart);
         if (j!=i) {        if  (cptcovn>0) {
           fprintf(ficres,"%1d%1d",i,j);          fprintf(ficresp, "\n#********** Variable "); 
           printf("%1d%1d",i,j);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           for(k=1; k<=ncovmodel;k++){          fprintf(ficresp, "**********\n#");
             printf(" %.5e",delti[jk]);        }
             fprintf(ficres," %.5e",delti[jk]);        for(i=1; i<=nlstate;i++) 
             jk++;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
           }        fprintf(ficresp, "\n");
           printf("\n");        
           fprintf(ficres,"\n");        for(i=iagemin; i <= iagemax+3; i++){
         }          if(i==iagemax+3){
       }            fprintf(ficlog,"Total");
       }          }else{
                if(first==1){
     k=1;              first=0;
     fprintf(ficres,"# Covariance\n");              printf("See log file for details...\n");
     printf("# Covariance\n");            }
     for(i=1;i<=npar;i++){            fprintf(ficlog,"Age %d", i);
       /*  if (k>nlstate) k=1;          }
       i1=(i-1)/(ncovmodel*nlstate)+1;          for(jk=1; jk <=nlstate ; jk++){
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       printf("%s%d%d",alph[k],i1,tab[i]);*/              pp[jk] += freq[jk][m][i]; 
       fprintf(ficres,"%3d",i);          }
       printf("%3d",i);          for(jk=1; jk <=nlstate ; jk++){
       for(j=1; j<=i;j++){            for(m=-1, pos=0; m <=0 ; m++)
         fprintf(ficres," %.5e",matcov[i][j]);              pos += freq[jk][m][i];
         printf(" %.5e",matcov[i][j]);            if(pp[jk]>=1.e-10){
       }              if(first==1){
       fprintf(ficres,"\n");              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       printf("\n");              }
       k++;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     }            }else{
                  if(first==1)
     while((c=getc(ficpar))=='#' && c!= EOF){                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       ungetc(c,ficpar);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       fgets(line, MAXLINE, ficpar);            }
       puts(line);          }
       fputs(line,ficparo);  
     }          for(jk=1; jk <=nlstate ; jk++){
     ungetc(c,ficpar);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
                pp[jk] += freq[jk][m][i];
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);          }       
              for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     if (fage <= 2) {            pos += pp[jk];
       bage = agemin;            posprop += prop[jk][i];
       fage = agemax;          }
     }          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");              if(first==1)
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 /*------------ gnuplot -------------*/              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 chdir(pathcd);            }else{
   if((ficgp=fopen("graph.plt","w"))==NULL) {              if(first==1)
     printf("Problem with file graph.gp");goto end;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 #ifdef windows            }
   fprintf(ficgp,"cd \"%s\" \n",pathc);            if( i <= iagemax){
 #endif              if(pos>=1.e-5){
 m=pow(2,cptcovn);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                  /*probs[i][jk][j1]= pp[jk]/pos;*/
  /* 1eme*/                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   for (cpt=1; cpt<= nlstate ; cpt ++) {              }
    for (k1=1; k1<= m ; k1 ++) {              else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
 #ifdef windows            }
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);          }
 #endif          
 #ifdef unix          for(jk=-1; jk <=nlstate+ndeath; jk++)
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);            for(m=-1; m <=nlstate+ndeath; m++)
 #endif              if(freq[jk][m][i] !=0 ) {
               if(first==1)
 for (i=1; i<= nlstate ; i ++) {                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   else fprintf(ficgp," \%%*lf (\%%*lf)");              }
 }          if(i <= iagemax)
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);            fprintf(ficresp,"\n");
     for (i=1; i<= nlstate ; i ++) {          if(first==1)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            printf("Others in log...\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficlog,"\n");
 }        }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      }
      for (i=1; i<= nlstate ; i ++) {    }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    dateintmean=dateintsum/k2cpt; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");   
 }      fclose(ficresp);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
 #ifdef unix    free_vector(pp,1,nlstate);
 fprintf(ficgp,"\nset ter gif small size 400,300");    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
 #endif    /* End of Freq */
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  }
    }  
   }  /************ Prevalence ********************/
   /*2 eme*/  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)
   {  
   for (k1=1; k1<= m ; k1 ++) {    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);       in each health status at the date of interview (if between dateprev1 and dateprev2).
           We still use firstpass and lastpass as another selection.
     for (i=1; i<= nlstate+1 ; i ++) {    */
       k=2*i;   
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
       for (j=1; j<= nlstate+1 ; j ++) {    double ***freq; /* Frequencies */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double *pp, **prop;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double pos,posprop; 
 }      double  y2; /* in fractional years */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    int iagemin, iagemax;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    iagemin= (int) agemin;
       for (j=1; j<= nlstate+1 ; j ++) {    iagemax= (int) agemax;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /*pp=vector(1,nlstate);*/
         else fprintf(ficgp," \%%*lf (\%%*lf)");    prop=matrix(1,nlstate,iagemin,iagemax+3); 
 }      /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       fprintf(ficgp,"\" t\"\" w l 0,");    j1=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 ++) {    j=cptcoveff;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   else fprintf(ficgp," \%%*lf (\%%*lf)");    
 }      for(k1=1; k1<=j;k1++){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      for(i1=1; i1<=ncodemax[k1];i1++){
       else fprintf(ficgp,"\" t\"\" w l 0,");        j1++;
     }        
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        for (i=1; i<=nlstate; i++)  
   }          for(m=iagemin; m <= iagemax+3; m++)
              prop[i][m]=0.0;
   /*3eme*/       
         for (i=1; i<=imx; i++) { /* Each individual */
    for (k1=1; k1<= m ; k1 ++) {          bool=1;
     for (cpt=1; cpt<= nlstate ; cpt ++) {          if  (cptcovn>0) {
       k=2+nlstate*(cpt-1);            for (z1=1; z1<=cptcoveff; z1++) 
       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 (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       for (i=1; i< nlstate ; i ++) {                bool=0;
         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);          } 
       }          if (bool==1) { 
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            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 */
    }              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                  if(agev[m][i]==0) agev[m][i]=iagemax+1;
   /* CV preval stat */                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     for (k1=1; k1<= m ; k1 ++) {                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); 
     for (cpt=1; cpt<nlstate ; cpt ++) {                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       k=3;                  /*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]]);*/
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       for (i=1; i< nlstate ; i ++)                  prop[s[m][i]][iagemax+3] += weight[i]; 
         fprintf(ficgp,"+$%d",k+i+1);                } 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              }
                  } /* end selection of waves */
       l=3+(nlstate+ndeath)*cpt;          }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        }
       for (i=1; i< nlstate ; i ++) {        for(i=iagemin; i <= iagemax+3; i++){  
         l=3+(nlstate+ndeath)*cpt;          
         fprintf(ficgp,"+$%d",l+i+1);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       }            posprop += prop[jk][i]; 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            } 
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }          for(jk=1; jk <=nlstate ; jk++){     
   }            if( i <=  iagemax){ 
                if(posprop>=1.e-5){ 
   /* proba elementaires */                probs[i][jk][j1]= prop[jk][i]/posprop;
   for(i=1,jk=1; i <=nlstate; i++){              } 
     for(k=1; k <=(nlstate+ndeath); k++){            } 
       if (k != i) {          }/* end jk */ 
         /*  fprintf(ficgp,"%1d%1d ",i,k);*/        }/* end i */ 
         for(j=1; j <=ncovmodel; j++){      } /* end i1 */
           fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);    } /* end k1 */
           jk++;    
           fprintf(ficgp,"\n");    /*  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);
     }  }  /* End of prevalence */
   }  
   for(jk=1; jk <=m; jk++) {  /************* Waves Concatenation ***************/
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);  
   for(i=1; i <=nlstate; i++) {  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(k=1; k <=(nlstate+ndeath); k++){  {
       if (k != i) {    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         fprintf(ficgp," exp(a%d%d+b%d%d*x",i,k,i,k);       Death is a valid wave (if date is known).
         for(j=3; j <=ncovmodel; j++)       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
           fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         fprintf(ficgp,")/(1");       and mw[mi+1][i]. dh depends on stepm.
         for(k1=1; k1 <=(nlstate+ndeath); k1++)       */
           if (k1 != i) {  
             fprintf(ficgp,"+exp(a%d%d+b%d%d*x",i,k1,i,k1);    int i, mi, m;
             for(j=3; j <=ncovmodel; j++)    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
               fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);       double sum=0., jmean=0.;*/
             fprintf(ficgp,")");    int first;
           }    int j, k=0,jk, ju, jl;
         fprintf(ficgp,") t \"p%d%d\" ", i,k);    double sum=0.;
       if ((i+k)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    first=0;
       }    jmin=1e+5;
     }    jmax=-1;
   }    jmean=0.;
 fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      for(i=1; i<=imx; i++){
   }      mi=0;
        m=firstpass;
  fclose(ficgp);      while(s[m][i] <= nlstate){
         if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
     chdir(path);          mw[++mi][i]=m;
     free_matrix(agev,1,maxwav,1,imx);        if(m >=lastpass)
     free_ivector(wav,1,imx);          break;
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        else
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          m++;
          }/* end while */
     free_imatrix(s,1,maxwav+1,1,n);      if (s[m][i] > nlstate){
            mi++;     /* Death is another wave */
            /* if(mi==0)  never been interviewed correctly before death */
     free_ivector(num,1,n);           /* Only death is a correct wave */
     free_vector(agedc,1,n);        mw[mi][i]=m;
     free_vector(weight,1,n);      }
     /*free_matrix(covar,1,NCOVMAX,1,n);*/  
     fclose(ficparo);      wav[i]=mi;
     fclose(ficres);      if(mi==0){
    }        nbwarn++;
            if(first==0){
    /*________fin mle=1_________*/          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
              first=1;
         }
          if(first==1){
     /* No more information from the sample is required now */          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
   /* Reads comments: lines beginning with '#' */        }
   while((c=getc(ficpar))=='#' && c!= EOF){      } /* end mi==0 */
     ungetc(c,ficpar);    } /* End individuals */
     fgets(line, MAXLINE, ficpar);  
     puts(line);    for(i=1; i<=imx; i++){
     fputs(line,ficparo);      for(mi=1; mi<wav[i];mi++){
   }        if (stepm <=0)
   ungetc(c,ficpar);          dh[mi][i]=1;
          else{
           if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);            if (agedc[i] < 2*AGESUP) {
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);              if(j==0) j=1;  /* Survives at least one month after exam */
 /*--------- index.htm --------*/              else if(j<0){
                 nberr++;
   if((fichtm=fopen("index.htm","w"))==NULL)    {                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]);
     printf("Problem with index.htm \n");goto end;                j=1; /* Temporary Dangerous patch */
   }                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                 fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
  fprintf(fichtm,"<body><ul> Imach, Version 0.63<hr> <li>Outputs files<br><br>\n                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);
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n              }
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>              k=k+1;
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>              if (j >= jmax){
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>                jmax=j;
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>                ijmax=i;
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>              }
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>              if (j <= jmin){
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>                jmin=j;
         - 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);                ijmin=i;
               }
  fprintf(fichtm," <li>Graphs</li>\n<p>");              sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
  m=cptcovn;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}            }
           }
  j1=0;          else{
  for(k1=1; k1<=m;k1++){            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
    for(i1=1; i1<=ncodemax[k1];i1++){  /*        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]); */
        j1++;  
        if (cptcovn > 0) {            k=k+1;
          fprintf(fichtm,"<hr>************ Results for covariates");            if (j >= jmax) {
          for (cpt=1; cpt<=cptcovn;cpt++)              jmax=j;
            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);              ijmax=i;
          fprintf(fichtm," ************\n<hr>");            }
        }            else if (j <= jmin){
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>              jmin=j;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);                  ijmin=i;
        for(cpt=1; cpt<nlstate;cpt++){            }
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
        }            if(j<0){
     for(cpt=1; cpt<=nlstate;cpt++) {              nberr++;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident              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]);
 interval) in state (%d): v%s%d%d.gif <br>              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]);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);              }
      }            sum=sum+j;
      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>          jk= j/stepm;
 <img src=\"ex%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          jl= j -jk*stepm;
      }          ju= j -(jk+1)*stepm;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
 health expectancies in states (1) and (2): e%s%d.gif<br>            if(jl==0){
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);              dh[mi][i]=jk;
 fprintf(fichtm,"\n</body>");              bh[mi][i]=0;
    }            }else{ /* We want a negative bias in order to only have interpolation ie
  }                    * at the price of an extra matrix product in likelihood */
 fclose(fichtm);              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
   /*--------------- Prevalence limit --------------*/            }
            }else{
   strcpy(filerespl,"pl");            if(jl <= -ju){
   strcat(filerespl,fileres);              dh[mi][i]=jk;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {              bh[mi][i]=jl;       /* bias is positive if real duration
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;                                   * is higher than the multiple of stepm and negative otherwise.
   }                                   */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);            }
   fprintf(ficrespl,"#Prevalence limit\n");            else{
   fprintf(ficrespl,"#Age ");              dh[mi][i]=jk+1;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);              bh[mi][i]=ju;
   fprintf(ficrespl,"\n");            }
              if(dh[mi][i]==0){
   prlim=matrix(1,nlstate,1,nlstate);              dh[mi][i]=1; /* At least one step */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              bh[mi][i]=ju; /* At least one step */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              /*  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);*/
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            }
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          } /* end if mle */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        }
   k=0;      } /* end wave */
   agebase=agemin;    }
   agelim=agemax;    jmean=sum/k;
   ftolpl=1.e-10;    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
   i1=cptcovn;    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
   if (cptcovn < 1){i1=1;}   }
   
   for(cptcov=1;cptcov<=i1;cptcov++){  /*********** Tricode ****************************/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  void tricode(int *Tvar, int **nbcode, int imx)
         k=k+1;  {
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    
         fprintf(ficrespl,"\n#****** ");    int Ndum[20],ij=1, k, j, i, maxncov=19;
         for(j=1;j<=cptcovn;j++)    int cptcode=0;
           fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);    cptcoveff=0; 
         fprintf(ficrespl,"******\n");   
            for (k=0; k<maxncov; k++) Ndum[k]=0;
         for (age=agebase; age<=agelim; age++){    for (k=1; k<=7; k++) ncodemax[k]=0;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
           fprintf(ficrespl,"%.0f",age );    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
           for(i=1; i<=nlstate;i++)      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
           fprintf(ficrespl," %.5f", prlim[i][i]);                                 modality*/ 
           fprintf(ficrespl,"\n");        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         }        Ndum[ij]++; /*store the modality */
       }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     }        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   fclose(ficrespl);                                         Tvar[j]. If V=sex and male is 0 and 
   /*------------- h Pij x at various ages ------------*/                                         female is 1, then  cptcode=1.*/
        }
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      for (i=0; i<=cptcode; i++) {
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        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 */
   }      }
   printf("Computing pij: result on file '%s' \n", filerespij);  
        ij=1; 
   stepsize=(int) (stepm+YEARM-1)/YEARM;      for (i=1; i<=ncodemax[j]; i++) {
   if (stepm<=24) stepsize=2;        for (k=0; k<= maxncov; k++) {
           if (Ndum[k] != 0) {
   agelim=AGESUP;            nbcode[Tvar[j]][ij]=k; 
   hstepm=stepsize*YEARM; /* Every year of age */            /* 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; */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */            
              ij++;
   k=0;          }
   for(cptcov=1;cptcov<=i1;cptcov++){          if (ij > ncodemax[j]) break; 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        }  
       k=k+1;      } 
         fprintf(ficrespij,"\n#****** ");    }  
         for(j=1;j<=cptcovn;j++)  
           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);   for (k=0; k< maxncov; k++) Ndum[k]=0;
         fprintf(ficrespij,"******\n");  
           for (i=1; i<=ncovmodel-2; i++) { 
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */     ij=Tvar[i];
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */     Ndum[ij]++;
           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);     ij=1;
           fprintf(ficrespij,"# Age");   for (i=1; i<= maxncov; i++) {
           for(i=1; i<=nlstate;i++)     if((Ndum[i]!=0) && (i<=ncovcol)){
             for(j=1; j<=nlstate+ndeath;j++)       Tvaraff[ij]=i; /*For printing */
               fprintf(ficrespij," %1d-%1d",i,j);       ij++;
           fprintf(ficrespij,"\n");     }
           for (h=0; h<=nhstepm; h++){   }
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );   
             for(i=1; i<=nlstate;i++)   cptcoveff=ij-1; /*Number of simple covariates*/
               for(j=1; j<=nlstate+ndeath;j++)  }
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
             fprintf(ficrespij,"\n");  /*********** Health Expectancies ****************/
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  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[] )
           fprintf(ficrespij,"\n");  
         }  {
     }    /* Health expectancies */
   }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     double age, agelim, hf;
   fclose(ficrespij);    double ***p3mat,***varhe;
     double **dnewm,**doldm;
   /*---------- Health expectancies and variances ------------*/    double *xp;
     double **gp, **gm;
   strcpy(filerest,"t");    double ***gradg, ***trgradg;
   strcat(filerest,fileres);    int theta;
   if((ficrest=fopen(filerest,"w"))==NULL) {  
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   }    xp=vector(1,npar);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
   strcpy(filerese,"e");    fprintf(ficreseij,"# Local time at start: %s", strstart);
   strcat(filerese,fileres);    fprintf(ficreseij,"# Health expectancies\n");
   if((ficreseij=fopen(filerese,"w"))==NULL) {    fprintf(ficreseij,"# Age");
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    for(i=1; i<=nlstate;i++)
   }      for(j=1; j<=nlstate;j++)
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     fprintf(ficreseij,"\n");
  strcpy(fileresv,"v");  
   strcat(fileresv,fileres);    if(estepm < stepm){
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      printf ("Problem %d lower than %d\n",estepm, stepm);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    }
   }    else  hstepm=estepm;   
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
   k=0;     * if stepm=24 months pijx are given only every 2 years and by summing them
   for(cptcov=1;cptcov<=i1;cptcov++){     * we are calculating an estimate of the Life Expectancy assuming a linear 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     * progression in between and thus overestimating or underestimating according
       k=k+1;     * to the curvature of the survival function. If, for the same date, we 
       fprintf(ficrest,"\n#****** ");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       for(j=1;j<=cptcovn;j++)     * to compare the new estimate of Life expectancy with the same linear 
         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);     * hypothesis. A more precise result, taking into account a more precise
       fprintf(ficrest,"******\n");     * curvature will be obtained if estepm is as small as stepm. */
   
       fprintf(ficreseij,"\n#****** ");    /* For example we decided to compute the life expectancy with the smallest unit */
       for(j=1;j<=cptcovn;j++)    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);       nhstepm is the number of hstepm from age to agelim 
       fprintf(ficreseij,"******\n");       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
       fprintf(ficresvij,"\n#****** ");       and note for a fixed period like estepm months */
       for(j=1;j<=cptcovn;j++)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);       survival function given by stepm (the optimization length). Unfortunately it
       fprintf(ficresvij,"******\n");       means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);       results. So we changed our mind and took the option of the best precision.
       oldm=oldms;savm=savms;    */
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;    agelim=AGESUP;
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
            /* nhstepm age range expressed in number of stepm */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       fprintf(ficrest,"\n");      /* if (stepm >= YEARM) hstepm=1;*/
              nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       hf=1;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       if (stepm >= YEARM) hf=stepm/YEARM;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       epj=vector(1,nlstate+1);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
       for(age=bage; age <=fage ;age++){      gm=matrix(0,nhstepm,1,nlstate*nlstate);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
         fprintf(ficrest," %.0f",age);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];   
           }  
           epj[nlstate+1] +=epj[j];      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         }  
         for(i=1, vepp=0.;i <=nlstate;i++)      /* Computing  Variances of health expectancies */
           for(j=1;j <=nlstate;j++)  
             vepp += vareij[i][j][(int)age];       for(theta=1; theta <=npar; theta++){
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));        for(i=1; i<=npar; i++){ 
         for(j=1;j <=nlstate;j++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));        }
         }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficrest,"\n");    
       }        cptj=0;
     }        for(j=1; j<= nlstate; j++){
   }          for(i=1; i<=nlstate; i++){
                    cptj=cptj+1;
  fclose(ficreseij);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
  fclose(ficresvij);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   fclose(ficrest);            }
   fclose(ficpar);          }
   free_vector(epj,1,nlstate+1);        }
   /*scanf("%d ",i); */       
        
   /*------- Variance limit prevalence------*/          for(i=1; i<=npar; i++) 
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
 strcpy(fileresvpl,"vpl");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   strcat(fileresvpl,fileres);        
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        cptj=0;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        for(j=1; j<= nlstate; j++){
     exit(0);          for(i=1;i<=nlstate;i++){
   }            cptj=cptj+1;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   
  k=0;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
  for(cptcov=1;cptcov<=i1;cptcov++){            }
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          }
      k=k+1;        }
      fprintf(ficresvpl,"\n#****** ");        for(j=1; j<= nlstate*nlstate; j++)
      for(j=1;j<=cptcovn;j++)          for(h=0; h<=nhstepm-1; h++){
        fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
      fprintf(ficresvpl,"******\n");          }
             } 
      varpl=matrix(1,nlstate,(int) bage, (int) fage);     
      oldm=oldms;savm=savms;  /* End theta */
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
    }       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
  }  
        for(h=0; h<=nhstepm-1; h++)
   fclose(ficresvpl);        for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
   /*---------- End : free ----------------*/            trgradg[h][j][theta]=gradg[h][theta][j];
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);       
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);       for(i=1;i<=nlstate*nlstate;i++)
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        for(j=1;j<=nlstate*nlstate;j++)
            varhe[i][j][(int)age] =0.;
    
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);       printf("%d|",(int)age);fflush(stdout);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);       for(h=0;h<=nhstepm-1;h++){
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        for(k=0;k<=nhstepm-1;k++){
            matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   free_matrix(matcov,1,npar,1,npar);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   free_vector(delti,1,npar);          for(i=1;i<=nlstate*nlstate;i++)
              for(j=1;j<=nlstate*nlstate;j++)
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
   printf("End of Imach\n");      }
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      /* Computing expectancies */
        for(i=1; i<=nlstate;i++)
   /* 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);*/        for(j=1; j<=nlstate;j++)
   /*printf("Total time was %d uSec.\n", total_usecs);*/          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   /*------ End -----------*/            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
  end:  /* 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]);*/
 #ifdef windows  
  chdir(pathcd);          }
 #endif  
  system("wgnuplot graph.plt");      fprintf(ficreseij,"%3.0f",age );
       cptj=0;
 #ifdef windows      for(i=1; i<=nlstate;i++)
   while (z[0] != 'q') {        for(j=1; j<=nlstate;j++){
     chdir(pathcd);          cptj++;
     printf("\nType e to edit output files, c to start again, and q for exiting: ");          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
     scanf("%s",z);        }
     if (z[0] == 'c') system("./imach");      fprintf(ficreseij,"\n");
     else if (z[0] == 'e') {     
       chdir(path);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       system("index.htm");      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     else if (z[0] == 'q') exit(0);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 #endif    }
 }    printf("\n");
     fprintf(ficlog,"\n");
   
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
   /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     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) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     /*  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;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs)))    {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
           if(line[j] == '\t')
             line[j] = ' ';
         }
         for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
           ;
         };
         line[j+1]=0;  /* Trims blanks at end of line */
         if(line[0]=='#'){
           fprintf(ficlog,"Comment line\n%s\n",line);
           printf("Comment line\n%s\n",line);
           continue;
         }
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); 
           errno=0;
           lval=strtol(strb,&endptr,10); 
           /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %d %s for individual %d\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n",lval, i,line,linei,j,maxwav);
             exit(1);
           }
           s[j][i]=lval;
   
           strcpy(line,stra);
           cutv(stra, strb,line,' ');
           if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
           }
           else  if(iout=sscanf(strb,".") != 0){
             month=99;
             year=9999;
           }else{
             printf("Error reading data around '%s'.at line number %ld %s for individual %d\nShould be a year of exam at wave %d.  Exiting.\n",strb, i,line,linei,j);
             exit(1);
           }
           anint[j][i]= (double) year; 
           mint[j][i]= (double)month; 
           strcpy(line,stra);
         } /* ENd Waves */
           
         cutv(stra, strb,line,' '); 
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,".") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s'.at line number %ld %s for individual %d\nShould be a year of exam at wave %d.  Exiting.\n",strb, i,line,linei,j);
           exit(1);
         }
         andc[i]=(double) year; 
         moisdc[i]=(double) month; 
         strcpy(line,stra);
   
         cutv(stra, strb,line,' '); 
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,".") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s'.at line number %ld %s for individual %d\nShould be a year of exam at wave %d.  Exiting.\n",strb, i,line,linei,j);
           exit(1);
         }
         annais[i]=(double)(year);
         moisnais[i]=(double)(month); 
         strcpy(line,stra);
   
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, i,line,linei);
           exit(1);
         }
         weight[i]=(double)(lval); 
         strcpy(line,stra);
   
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); 
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, i,line,linei);
             exit(1);
           }
           if(lval <-1 || lval >1){
             printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,i,line,linei,j);
             exit(1);
           }
           covar[j][i]=(double)(lval);
           strcpy(line,stra);
         } 
         lstra=strlen(stra);
   
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
     } /* End loop reading  data */
     /* 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 (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.1; p[NDIM]=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.1.110


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