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version 1.2, 2001/03/13 18:10:26 version 1.97, 2004/02/20 13:25:42
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      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.97  2004/02/20 13:25:42  lievre
   individuals from different ages are interviewed on their health status    Version 0.96d. Population forecasting command line is (temporarily)
   or degree of  disability. At least a second wave of interviews    suppressed.
   ("longitudinal") should  measure each new individual health status.  
   Health expectancies are computed from the transistions observed between    Revision 1.96  2003/07/15 15:38:55  brouard
   waves and are computed for each degree of severity of disability (number    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   of life states). More degrees you consider, more time is necessary to    rewritten within the same printf. Workaround: many printfs.
   reach the Maximum Likelihood of the parameters involved in the model.  
   The simplest model is the multinomial logistic model where pij is    Revision 1.95  2003/07/08 07:54:34  brouard
   the probabibility to be observed in state j at the second wave conditional    * imach.c (Repository):
   to be observed in state i at the first wave. Therefore the model is:    (Repository): Using imachwizard code to output a more meaningful covariance
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    matrix (cov(a12,c31) instead of numbers.
   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 1.94  2003/06/27 13:00:02  brouard
     *Covariates have to be included here again* invites you to do it.    Just cleaning
   More covariates you add, less is the speed of the convergence.  
     Revision 1.93  2003/06/25 16:33:55  brouard
   The advantage that this computer programme claims, comes from that if the    (Module): On windows (cygwin) function asctime_r doesn't
   delay between waves is not identical for each individual, or if some    exist so I changed back to asctime which exists.
   individual missed an interview, the information is not rounded or lost, but    (Module): Version 0.96b
   taken into account using an interpolation or extrapolation.  
   hPijx is the probability to be    Revision 1.92  2003/06/25 16:30:45  brouard
   observed in state i at age x+h conditional to the observed state i at age    (Module): On windows (cygwin) function asctime_r doesn't
   x. The delay 'h' can be split into an exact number (nh*stepm) of    exist so I changed back to asctime which exists.
   unobserved intermediate  states. This elementary transition (by month or  
   quarter trimester, semester or year) is model as a multinomial logistic.    Revision 1.91  2003/06/25 15:30:29  brouard
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    * imach.c (Repository): Duplicated warning errors corrected.
   and the contribution of each individual to the likelihood is simply hPijx.    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
   Also this programme outputs the covariance matrix of the parameters but also    is stamped in powell.  We created a new html file for the graphs
   of the life expectancies. It also computes the prevalence limits.    concerning matrix of covariance. It has extension -cov.htm.
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.90  2003/06/24 12:34:15  brouard
            Institut national d'études démographiques, Paris.    (Module): Some bugs corrected for windows. Also, when
   This software have been partly granted by Euro-REVES, a concerted action    mle=-1 a template is output in file "or"mypar.txt with the design
   from the European Union.    of the covariance matrix to be input.
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.89  2003/06/24 12:30:52  brouard
   can be accessed at http://euroreves.ined.fr/imach .    (Module): Some bugs corrected for windows. Also, when
   **********************************************************************/    mle=-1 a template is output in file "or"mypar.txt with the design
      of the covariance matrix to be input.
 #include <math.h>  
 #include <stdio.h>    Revision 1.88  2003/06/23 17:54:56  brouard
 #include <stdlib.h>    * 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.
 #include <unistd.h>  
     Revision 1.87  2003/06/18 12:26:01  brouard
 #define MAXLINE 256    Version 0.96
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.86  2003/06/17 20:04:08  brouard
 #define windows    (Module): Change position of html and gnuplot routines and added
     routine fileappend.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
 #define NINTERVMAX 8    current date of interview. It may happen when the death was just
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    prior to the death. In this case, dh was negative and likelihood
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    was wrong (infinity). We still send an "Error" but patch by
 #define NCOVMAX 8 /* Maximum number of covariates */    assuming that the date of death was just one stepm after the
 #define MAXN 80000    interview.
 #define YEARM 12. /* Number of months per year */    (Repository): Because some people have very long ID (first column)
 #define AGESUP 130    we changed int to long in num[] and we added a new lvector for
 #define AGEBASE 40    memory allocation. But we also truncated to 8 characters (left
     truncation)
     (Repository): No more line truncation errors.
 int nvar;  
 static int cptcov;    Revision 1.84  2003/06/13 21:44:43  brouard
 int cptcovn;    * imach.c (Repository): Replace "freqsummary" at a correct
 int npar=NPARMAX;    place. It differs from routine "prevalence" which may be called
 int nlstate=2; /* Number of live states */    many times. Probs is memory consuming and must be used with
 int ndeath=1; /* Number of dead states */    parcimony.
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.83  2003/06/10 13:39:11  lievre
 int maxwav; /* Maxim number of waves */    *** empty log message ***
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.82  2003/06/05 15:57:20  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Add log in  imach.c and  fullversion number is now printed.
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;  /*
 FILE *ficgp, *fichtm;     Interpolated Markov Chain
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Short summary of the programme:
  FILE  *ficresvij;    
   char fileresv[FILENAMELENGTH];    This program computes Healthy Life Expectancies from
  FILE  *ficresvpl;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   char fileresvpl[FILENAMELENGTH];    first survey ("cross") where individuals from different ages are
     interviewed on their health status or degree of disability (in the
     case of a health survey which is our main interest) -2- at least a
     second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
 #define NR_END 1    computed from the time spent in each health state according to a
 #define FREE_ARG char*    model. More health states you consider, more time is necessary to reach the
 #define FTOL 1.0e-10    Maximum Likelihood of the parameters involved in the model.  The
     simplest model is the multinomial logistic model where pij is the
 #define NRANSI    probability to be observed in state j at the second wave
 #define ITMAX 200    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
 #define TOL 2.0e-4    '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
 #define CGOLD 0.3819660    where the markup *Covariates have to be included here again* invites
 #define ZEPS 1.0e-10    you to do it.  More covariates you add, slower the
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    convergence.
   
 #define GOLD 1.618034    The advantage of this computer programme, compared to a simple
 #define GLIMIT 100.0    multinomial logistic model, is clear when the delay between waves is not
 #define TINY 1.0e-20    identical for each individual. Also, if a individual missed an
     intermediate interview, the information is lost, but taken into
 static double maxarg1,maxarg2;    account using an interpolation or extrapolation.  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    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
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    split into an exact number (nh*stepm) of unobserved intermediate
 #define rint(a) floor(a+0.5)    states. This elementary transition (by month, quarter,
     semester or year) is modelled as a multinomial logistic.  The hPx
 static double sqrarg;    matrix is simply the matrix product of nh*stepm elementary matrices
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    and the contribution of each individual to the likelihood is simply
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    hPijx.
   
 int imx;    Also this programme outputs the covariance matrix of the parameters but also
 int stepm;    of the life expectancies. It also computes the stable prevalence. 
 /* Stepm, step in month: minimum step interpolation*/    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 int m,nb;             Institut national d'études démographiques, Paris.
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax;    This software have been partly granted by Euro-REVES, a concerted action
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    from the European Union.
 double **pmmij;    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 double *weight;    can be accessed at http://euroreves.ined.fr/imach .
 int **s; /* Status */  
 double *agedc, **covar, idx;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 int **nbcode, *Tcode, *Tvar, **codtab;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    **********************************************************************/
 double ftolhess; /* Tolerance for computing hessian */  /*
     main
     read parameterfile
 /******************************************/    read datafile
     concatwav
 void replace(char *s, char*t)    freqsummary
 {    if (mle >= 1)
   int i;      mlikeli
   int lg=20;    print results files
   i=0;    if mle==1 
   lg=strlen(t);       computes hessian
   for(i=0; i<= lg; i++) {    read end of parameter file: agemin, agemax, bage, fage, estepm
     (s[i] = t[i]);        begin-prev-date,...
     if (t[i]== '\\') s[i]='/';    open gnuplot file
   }    open html file
 }    stable prevalence
      for age prevalim()
 int nbocc(char *s, char occ)    h Pij x
 {    variance of p varprob
   int i,j=0;    forecasting if prevfcast==1 prevforecast call prevalence()
   int lg=20;    health expectancies
   i=0;    Variance-covariance of DFLE
   lg=strlen(s);    prevalence()
   for(i=0; i<= lg; i++) {     movingaverage()
   if  (s[i] == occ ) j++;    varevsij() 
   }    if popbased==1 varevsij(,popbased)
   return j;    total life expectancies
 }    Variance of stable prevalence
    end
 void cutv(char *u,char *v, char*t, char occ)  */
 {  
   int i,lg,j,p;  
   i=0;  
   if (t[0]== occ) p=0;   
   for(j=0; j<=strlen(t)-1; j++) {  #include <math.h>
     if((t[j]!= occ) && (t[j+1]==occ)) p=j+1;  #include <stdio.h>
   }  #include <stdlib.h>
   #include <unistd.h>
   lg=strlen(t);  
   for(j=0; j<p; j++) {  #include <sys/time.h>
     (u[j] = t[j]);  #include <time.h>
     u[p]='\0';  #include "timeval.h"
   }  
   /* #include <libintl.h> */
    for(j=0; j<= lg; j++) {  /* #define _(String) gettext (String) */
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }  #define MAXLINE 256
 }  #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
 /********************** nrerror ********************/  /*#define DEBUG*/
   /*#define windows*/
 void nrerror(char error_text[])  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 {  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   exit(1);  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 }  
 /*********************** vector *******************/  #define NINTERVMAX 8
 double *vector(int nl, int nh)  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 {  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   double *v;  #define NCOVMAX 8 /* Maximum number of covariates */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #define MAXN 20000
   if (!v) nrerror("allocation failure in vector");  #define YEARM 12. /* Number of months per year */
   return v-nl+NR_END;  #define AGESUP 130
 }  #define AGEBASE 40
   #ifdef unix
 /************************ free vector ******************/  #define DIRSEPARATOR '/'
 void free_vector(double*v, int nl, int nh)  #define ODIRSEPARATOR '\\'
 {  #else
   free((FREE_ARG)(v+nl-NR_END));  #define DIRSEPARATOR '\\'
 }  #define ODIRSEPARATOR '/'
   #endif
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  /* $Id$ */
 {  /* $State$ */
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  char version[]="Imach version 0.96d, February 2004, INED-EUROREVES ";
   if (!v) nrerror("allocation failure in ivector");  char fullversion[]="$Revision$ $Date$"; 
   return v-nl+NR_END;  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 }  int nvar;
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 /******************free ivector **************************/  int npar=NPARMAX;
 void free_ivector(int *v, long nl, long nh)  int nlstate=2; /* Number of live states */
 {  int ndeath=1; /* Number of dead states */
   free((FREE_ARG)(v+nl-NR_END));  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 }  int popbased=0;
   
 /******************* imatrix *******************************/  int *wav; /* Number of waves for this individuual 0 is possible */
 int **imatrix(long nrl, long nrh, long ncl, long nch)  int maxwav; /* Maxim number of waves */
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  int jmin, jmax; /* min, max spacing between 2 waves */
 {  int gipmx, gsw; /* Global variables on the number of contributions 
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;                     to the likelihood and the sum of weights (done by funcone)*/
   int **m;  int mle, weightopt;
    int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   /* allocate pointers to rows */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   if (!m) nrerror("allocation failure 1 in matrix()");             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   m += NR_END;  double jmean; /* Mean space between 2 waves */
   m -= nrl;  double **oldm, **newm, **savm; /* Working pointers to matrices */
    double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
    FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   /* allocate rows and set pointers to them */  FILE *ficlog, *ficrespow;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  int globpr; /* Global variable for printing or not */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double fretone; /* Only one call to likelihood */
   m[nrl] += NR_END;  long ipmx; /* Number of contributions */
   m[nrl] -= ncl;  double sw; /* Sum of weights */
    char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  FILE *ficresilk;
    FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   /* return pointer to array of pointers to rows */  FILE *ficresprobmorprev;
   return m;  FILE *fichtm, *fichtmcov; /* Html File */
 }  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 /****************** free_imatrix *************************/  FILE  *ficresvij;
 void free_imatrix(m,nrl,nrh,ncl,nch)  char fileresv[FILENAMELENGTH];
       int **m;  FILE  *ficresvpl;
       long nch,ncl,nrh,nrl;  char fileresvpl[FILENAMELENGTH];
      /* free an int matrix allocated by imatrix() */  char title[MAXLINE];
 {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   free((FREE_ARG) (m+nrl-NR_END));  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 }  char command[FILENAMELENGTH];
   int  outcmd=0;
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  char filelog[FILENAMELENGTH]; /* Log file */
   double **m;  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char popfile[FILENAMELENGTH];
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   m -= nrl;  
   struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  struct timezone tzp;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  extern int gettimeofday();
   m[nrl] += NR_END;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   m[nrl] -= ncl;  long time_value;
   extern long time();
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  char strcurr[80], strfor[80];
   return m;  
 }  #define NR_END 1
   #define FREE_ARG char*
 /*************************free matrix ************************/  #define FTOL 1.0e-10
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {  #define NRANSI 
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define ITMAX 200 
   free((FREE_ARG)(m+nrl-NR_END));  
 }  #define TOL 2.0e-4 
   
 /******************* ma3x *******************************/  #define CGOLD 0.3819660 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  #define ZEPS 1.0e-10 
 {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  #define GOLD 1.618034 
   #define GLIMIT 100.0 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define TINY 1.0e-20 
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  static double maxarg1,maxarg2;
   m -= nrl;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   m[nrl] += NR_END;  #define rint(a) floor(a+0.5)
   m[nrl] -= ncl;  
   static double sqrarg;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  int imx; 
   m[nrl][ncl] += NR_END;  int stepm;
   m[nrl][ncl] -= nll;  /* Stepm, step in month: minimum step interpolation*/
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;  int estepm;
    /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  int m,nb;
     for (j=ncl+1; j<=nch; j++)  long *num;
       m[i][j]=m[i][j-1]+nlay;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   }  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   return m;  double **pmmij, ***probs;
 }  double dateintmean=0;
   
 /*************************free ma3x ************************/  double *weight;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  int **s; /* Status */
 {  double *agedc, **covar, idx;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 }  double ftolhess; /* Tolerance for computing hessian */
   
 /***************** f1dim *************************/  /**************** split *************************/
 extern int ncom;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 extern double *pcom,*xicom;  {
 extern double (*nrfunc)(double []);    char  *ss;                            /* pointer */
      int   l1, l2;                         /* length counters */
 double f1dim(double x)  
 {    l1 = strlen(path );                   /* length of path */
   int j;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   double f;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   double *xt;    if ( ss == NULL ) {                   /* no directory, so use current */
        /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   xt=vector(1,ncom);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];      /* get current working directory */
   f=(*nrfunc)(xt);      /*    extern  char* getcwd ( char *buf , int len);*/
   free_vector(xt,1,ncom);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   return f;        return( GLOCK_ERROR_GETCWD );
 }      }
       strcpy( name, path );               /* we've got it */
 /*****************brent *************************/    } else {                              /* strip direcotry from path */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)      ss++;                               /* after this, the filename */
 {      l2 = strlen( ss );                  /* length of filename */
   int iter;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   double a,b,d,etemp;      strcpy( name, ss );         /* save file name */
   double fu,fv,fw,fx;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   double ftemp;      dirc[l1-l2] = 0;                    /* add zero */
   double p,q,r,tol1,tol2,u,v,w,x,xm;    }
   double e=0.0;    l1 = strlen( dirc );                  /* length of directory */
      /*#ifdef windows
   a=(ax < cx ? ax : cx);    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   b=(ax > cx ? ax : cx);  #else
   x=w=v=bx;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   fw=fv=fx=(*f)(x);  #endif
   for (iter=1;iter<=ITMAX;iter++) {    */
     xm=0.5*(a+b);    ss = strrchr( name, '.' );            /* find last / */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    ss++;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    strcpy(ext,ss);                       /* save extension */
     printf(".");fflush(stdout);    l1= strlen( name);
 #ifdef DEBUG    l2= strlen(ss)+1;
     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);    strncpy( finame, name, l1-l2);
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    finame[l1-l2]= 0;
 #endif    return( 0 );                          /* we're done */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  }
       *xmin=x;  
       return fx;  
     }  /******************************************/
     ftemp=fu;  
     if (fabs(e) > tol1) {  void replace_back_to_slash(char *s, char*t)
       r=(x-w)*(fx-fv);  {
       q=(x-v)*(fx-fw);    int i;
       p=(x-v)*q-(x-w)*r;    int lg=0;
       q=2.0*(q-r);    i=0;
       if (q > 0.0) p = -p;    lg=strlen(t);
       q=fabs(q);    for(i=0; i<= lg; i++) {
       etemp=e;      (s[i] = t[i]);
       e=d;      if (t[i]== '\\') s[i]='/';
       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));  }
       else {  
         d=p/q;  int nbocc(char *s, char occ)
         u=x+d;  {
         if (u-a < tol2 || b-u < tol2)    int i,j=0;
           d=SIGN(tol1,xm-x);    int lg=20;
       }    i=0;
     } else {    lg=strlen(s);
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    for(i=0; i<= lg; i++) {
     }    if  (s[i] == occ ) j++;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    }
     fu=(*f)(u);    return j;
     if (fu <= fx) {  }
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  void cutv(char *u,char *v, char*t, char occ)
         SHFT(fv,fw,fx,fu)  {
         } else {    /* cuts string t into u and v where u is ended by char occ excluding it
           if (u < x) a=u; else b=u;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
           if (fu <= fw || w == x) {       gives u="abcedf" and v="ghi2j" */
             v=w;    int i,lg,j,p=0;
             w=u;    i=0;
             fv=fw;    for(j=0; j<=strlen(t)-1; j++) {
             fw=fu;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
           } else if (fu <= fv || v == x || v == w) {    }
             v=u;  
             fv=fu;    lg=strlen(t);
           }    for(j=0; j<p; j++) {
         }      (u[j] = t[j]);
   }    }
   nrerror("Too many iterations in brent");       u[p]='\0';
   *xmin=x;  
   return fx;     for(j=0; j<= lg; j++) {
 }      if (j>=(p+1))(v[j-p-1] = t[j]);
     }
 /****************** mnbrak ***********************/  }
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  /********************** nrerror ********************/
             double (*func)(double))  
 {  void nrerror(char error_text[])
   double ulim,u,r,q, dum;  {
   double fu;    fprintf(stderr,"ERREUR ...\n");
      fprintf(stderr,"%s\n",error_text);
   *fa=(*func)(*ax);    exit(EXIT_FAILURE);
   *fb=(*func)(*bx);  }
   if (*fb > *fa) {  /*********************** vector *******************/
     SHFT(dum,*ax,*bx,dum)  double *vector(int nl, int nh)
       SHFT(dum,*fb,*fa,dum)  {
       }    double *v;
   *cx=(*bx)+GOLD*(*bx-*ax);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   *fc=(*func)(*cx);    if (!v) nrerror("allocation failure in vector");
   while (*fb > *fc) {    return v-nl+NR_END;
     r=(*bx-*ax)*(*fb-*fc);  }
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  /************************ free vector ******************/
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  void free_vector(double*v, int nl, int nh)
     ulim=(*bx)+GLIMIT*(*cx-*bx);  {
     if ((*bx-u)*(u-*cx) > 0.0) {    free((FREE_ARG)(v+nl-NR_END));
       fu=(*func)(u);  }
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  /************************ivector *******************************/
       if (fu < *fc) {  int *ivector(long nl,long nh)
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  {
           SHFT(*fb,*fc,fu,(*func)(u))    int *v;
           }    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    if (!v) nrerror("allocation failure in ivector");
       u=ulim;    return v-nl+NR_END;
       fu=(*func)(u);  }
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);  /******************free ivector **************************/
       fu=(*func)(u);  void free_ivector(int *v, long nl, long nh)
     }  {
     SHFT(*ax,*bx,*cx,u)    free((FREE_ARG)(v+nl-NR_END));
       SHFT(*fa,*fb,*fc,fu)  }
       }  
 }  /************************lvector *******************************/
   long *lvector(long nl,long nh)
 /*************** linmin ************************/  {
     long *v;
 int ncom;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 double *pcom,*xicom;    if (!v) nrerror("allocation failure in ivector");
 double (*nrfunc)(double []);    return v-nl+NR_END;
    }
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {  /******************free lvector **************************/
   double brent(double ax, double bx, double cx,  void free_lvector(long *v, long nl, long nh)
                double (*f)(double), double tol, double *xmin);  {
   double f1dim(double x);    free((FREE_ARG)(v+nl-NR_END));
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  }
               double *fc, double (*func)(double));  
   int j;  /******************* imatrix *******************************/
   double xx,xmin,bx,ax;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   double fx,fb,fa;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
    { 
   ncom=n;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   pcom=vector(1,n);    int **m; 
   xicom=vector(1,n);    
   nrfunc=func;    /* allocate pointers to rows */ 
   for (j=1;j<=n;j++) {    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     pcom[j]=p[j];    if (!m) nrerror("allocation failure 1 in matrix()"); 
     xicom[j]=xi[j];    m += NR_END; 
   }    m -= nrl; 
   ax=0.0;    
   xx=1.0;    
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    /* allocate rows and set pointers to them */ 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 #ifdef DEBUG    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    m[nrl] += NR_END; 
 #endif    m[nrl] -= ncl; 
   for (j=1;j<=n;j++) {    
     xi[j] *= xmin;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     p[j] += xi[j];    
   }    /* return pointer to array of pointers to rows */ 
   free_vector(xicom,1,n);    return m; 
   free_vector(pcom,1,n);  } 
 }  
   /****************** free_imatrix *************************/
 /*************** powell ************************/  void free_imatrix(m,nrl,nrh,ncl,nch)
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,        int **m;
             double (*func)(double []))        long nch,ncl,nrh,nrl; 
 {       /* free an int matrix allocated by imatrix() */ 
   void linmin(double p[], double xi[], int n, double *fret,  { 
               double (*func)(double []));    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   int i,ibig,j;    free((FREE_ARG) (m+nrl-NR_END)); 
   double del,t,*pt,*ptt,*xit;  } 
   double fp,fptt;  
   double *xits;  /******************* matrix *******************************/
   pt=vector(1,n);  double **matrix(long nrl, long nrh, long ncl, long nch)
   ptt=vector(1,n);  {
   xit=vector(1,n);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   xits=vector(1,n);    double **m;
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   for (*iter=1;;++(*iter)) {    if (!m) nrerror("allocation failure 1 in matrix()");
     fp=(*fret);    m += NR_END;
     ibig=0;    m -= nrl;
     del=0.0;  
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     for (i=1;i<=n;i++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       printf(" %d %.12f",i, p[i]);    m[nrl] += NR_END;
     printf("\n");    m[nrl] -= ncl;
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       fptt=(*fret);    return m;
 #ifdef DEBUG    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       printf("fret=%lf \n",*fret);     */
 #endif  }
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  /*************************free matrix ************************/
       if (fabs(fptt-(*fret)) > del) {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
         del=fabs(fptt-(*fret));  {
         ibig=i;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       }    free((FREE_ARG)(m+nrl-NR_END));
 #ifdef DEBUG  }
       printf("%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {  /******************* ma3x *******************************/
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
         printf(" x(%d)=%.12e",j,xit[j]);  {
       }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       for(j=1;j<=n;j++)    double ***m;
         printf(" p=%.12e",p[j]);  
       printf("\n");    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 #endif    if (!m) nrerror("allocation failure 1 in matrix()");
     }    m += NR_END;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    m -= nrl;
 #ifdef DEBUG  
       int k[2],l;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       k[0]=1;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       k[1]=-1;    m[nrl] += NR_END;
       printf("Max: %.12e",(*func)(p));    m[nrl] -= ncl;
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       printf("\n");  
       for(l=0;l<=1;l++) {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         for (j=1;j<=n;j++) {    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    m[nrl][ncl] += 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]);    m[nrl][ncl] -= nll;
         }    for (j=ncl+1; j<=nch; j++) 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));      m[nrl][j]=m[nrl][j-1]+nlay;
       }    
 #endif    for (i=nrl+1; i<=nrh; i++) {
       m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       for (j=ncl+1; j<=nch; j++) 
       free_vector(xit,1,n);        m[i][j]=m[i][j-1]+nlay;
       free_vector(xits,1,n);    }
       free_vector(ptt,1,n);    return m; 
       free_vector(pt,1,n);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       return;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     }    */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  }
     for (j=1;j<=n;j++) {  
       ptt[j]=2.0*p[j]-pt[j];  /*************************free ma3x ************************/
       xit[j]=p[j]-pt[j];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       pt[j]=p[j];  {
     }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     fptt=(*func)(ptt);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     if (fptt < fp) {    free((FREE_ARG)(m+nrl-NR_END));
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  }
       if (t < 0.0) {  
         linmin(p,xit,n,fret,func);  /*************** function subdirf ***********/
         for (j=1;j<=n;j++) {  char *subdirf(char fileres[])
           xi[j][ibig]=xi[j][n];  {
           xi[j][n]=xit[j];    /* Caution optionfilefiname is hidden */
         }    strcpy(tmpout,optionfilefiname);
 #ifdef DEBUG    strcat(tmpout,"/"); /* Add to the right */
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    strcat(tmpout,fileres);
         for(j=1;j<=n;j++)    return tmpout;
           printf(" %.12e",xit[j]);  }
         printf("\n");  
 #endif  /*************** function subdirf2 ***********/
       }  char *subdirf2(char fileres[], char *preop)
     }  {
   }    
 }    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
 /**** Prevalence limit ****************/    strcat(tmpout,"/");
     strcat(tmpout,preop);
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    strcat(tmpout,fileres);
 {    return tmpout;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  }
      matrix by transitions matrix until convergence is reached */  
   /*************** function subdirf3 ***********/
   int i, ii,j,k;  char *subdirf3(char fileres[], char *preop, char *preop2)
   double min, max, maxmin, maxmax,sumnew=0.;  {
   double **matprod2();    
   double **out, cov[NCOVMAX], **pmij();    /* Caution optionfilefiname is hidden */
   double **newm;    strcpy(tmpout,optionfilefiname);
   double agefin, delaymax=50 ; /* Max number of years to converge */    strcat(tmpout,"/");
     strcat(tmpout,preop);
   for (ii=1;ii<=nlstate+ndeath;ii++)    strcat(tmpout,preop2);
     for (j=1;j<=nlstate+ndeath;j++){    strcat(tmpout,fileres);
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    return tmpout;
     }  }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  /***************** f1dim *************************/
     newm=savm;  extern int ncom; 
     /* Covariates have to be included here again */  extern double *pcom,*xicom;
     cov[1]=1.;  extern double (*nrfunc)(double []); 
     cov[2]=agefin;   
     if (cptcovn>0){  double f1dim(double x) 
       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]]);*/}  { 
     }    int j; 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    double f;
     double *xt; 
     savm=oldm;   
     oldm=newm;    xt=vector(1,ncom); 
     maxmax=0.;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     for(j=1;j<=nlstate;j++){    f=(*nrfunc)(xt); 
       min=1.;    free_vector(xt,1,ncom); 
       max=0.;    return f; 
       for(i=1; i<=nlstate; i++) {  } 
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  /*****************brent *************************/
         prlim[i][j]= newm[i][j]/(1-sumnew);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
         max=FMAX(max,prlim[i][j]);  { 
         min=FMIN(min,prlim[i][j]);    int iter; 
       }    double a,b,d,etemp;
       maxmin=max-min;    double fu,fv,fw,fx;
       maxmax=FMAX(maxmax,maxmin);    double ftemp;
     }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     if(maxmax < ftolpl){    double e=0.0; 
       return prlim;   
     }    a=(ax < cx ? ax : cx); 
   }    b=(ax > cx ? ax : cx); 
 }    x=w=v=bx; 
     fw=fv=fx=(*f)(x); 
 /*************** transition probabilities **********/    for (iter=1;iter<=ITMAX;iter++) { 
       xm=0.5*(a+b); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 {      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   double s1, s2;      printf(".");fflush(stdout);
   /*double t34;*/      fprintf(ficlog,".");fflush(ficlog);
   int i,j,j1, nc, ii, jj;  #ifdef DEBUG
       printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     for(i=1; i<= nlstate; i++){      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     for(j=1; j<i;j++){      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #endif
         /*s2 += param[i][j][nc]*cov[nc];*/      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        *xmin=x; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/        return fx; 
       }      } 
       ps[i][j]=s2;      ftemp=fu;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      if (fabs(e) > tol1) { 
     }        r=(x-w)*(fx-fv); 
     for(j=i+1; j<=nlstate+ndeath;j++){        q=(x-v)*(fx-fw); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        p=(x-v)*q-(x-w)*r; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        q=2.0*(q-r); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        if (q > 0.0) p = -p; 
       }        q=fabs(q); 
       ps[i][j]=s2;        etemp=e; 
     }        e=d; 
   }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   for(i=1; i<= nlstate; i++){          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
      s1=0;        else { 
     for(j=1; j<i; j++)          d=p/q; 
       s1+=exp(ps[i][j]);          u=x+d; 
     for(j=i+1; j<=nlstate+ndeath; j++)          if (u-a < tol2 || b-u < tol2) 
       s1+=exp(ps[i][j]);            d=SIGN(tol1,xm-x); 
     ps[i][i]=1./(s1+1.);        } 
     for(j=1; j<i; j++)      } else { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     for(j=i+1; j<=nlstate+ndeath; j++)      } 
       ps[i][j]= exp(ps[i][j])*ps[i][i];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      fu=(*f)(u); 
   } /* end i */      if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        SHFT(v,w,x,u) 
     for(jj=1; jj<= nlstate+ndeath; jj++){          SHFT(fv,fw,fx,fu) 
       ps[ii][jj]=0;          } else { 
       ps[ii][ii]=1;            if (u < x) a=u; else b=u; 
     }            if (fu <= fw || w == x) { 
   }              v=w; 
               w=u; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){              fv=fw; 
     for(jj=1; jj<= nlstate+ndeath; jj++){              fw=fu; 
      printf("%lf ",ps[ii][jj]);            } else if (fu <= fv || v == x || v == w) { 
    }              v=u; 
     printf("\n ");              fv=fu; 
     }            } 
     printf("\n ");printf("%lf ",cov[2]);*/          } 
 /*    } 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    nrerror("Too many iterations in brent"); 
   goto end;*/    *xmin=x; 
     return ps;    return fx; 
 }  } 
   
 /**************** Product of 2 matrices ******************/  /****************** mnbrak ***********************/
   
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
 {              double (*func)(double)) 
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  { 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    double ulim,u,r,q, dum;
   /* in, b, out are matrice of pointers which should have been initialized    double fu; 
      before: only the contents of out is modified. The function returns   
      a pointer to pointers identical to out */    *fa=(*func)(*ax); 
   long i, j, k;    *fb=(*func)(*bx); 
   for(i=nrl; i<= nrh; i++)    if (*fb > *fa) { 
     for(k=ncolol; k<=ncoloh; k++)      SHFT(dum,*ax,*bx,dum) 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        SHFT(dum,*fb,*fa,dum) 
         out[i][k] +=in[i][j]*b[j][k];        } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
   return out;    *fc=(*func)(*cx); 
 }    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
 /************* Higher Matrix Product ***************/      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 {      if ((*bx-u)*(u-*cx) > 0.0) { 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        fu=(*func)(u); 
      duration (i.e. until      } else if ((*cx-u)*(u-ulim) > 0.0) { 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        fu=(*func)(u); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        if (fu < *fc) { 
      (typically every 2 years instead of every month which is too big).          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
      Model is determined by parameters x and covariates have to be            SHFT(*fb,*fc,fu,(*func)(u)) 
      included manually here.            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
      */        u=ulim; 
         fu=(*func)(u); 
   int i, j, d, h, k;      } else { 
   double **out, cov[NCOVMAX];        u=(*cx)+GOLD*(*cx-*bx); 
   double **newm;        fu=(*func)(u); 
       } 
   /* Hstepm could be zero and should return the unit matrix */      SHFT(*ax,*bx,*cx,u) 
   for (i=1;i<=nlstate+ndeath;i++)        SHFT(*fa,*fb,*fc,fu) 
     for (j=1;j<=nlstate+ndeath;j++){        } 
       oldm[i][j]=(i==j ? 1.0 : 0.0);  } 
       po[i][j][0]=(i==j ? 1.0 : 0.0);  
     }  /*************** linmin ************************/
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(h=1; h <=nhstepm; h++){  int ncom; 
     for(d=1; d <=hstepm; d++){  double *pcom,*xicom;
       newm=savm;  double (*nrfunc)(double []); 
       /* Covariates have to be included here again */   
       cov[1]=1.;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  { 
       if (cptcovn>0){    double brent(double ax, double bx, double cx, 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];                 double (*f)(double), double tol, double *xmin); 
     }    double f1dim(double x); 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/                double *fc, double (*func)(double)); 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    int j; 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    double xx,xmin,bx,ax; 
       savm=oldm;    double fx,fb,fa;
       oldm=newm;   
     }    ncom=n; 
     for(i=1; i<=nlstate+ndeath; i++)    pcom=vector(1,n); 
       for(j=1;j<=nlstate+ndeath;j++) {    xicom=vector(1,n); 
         po[i][j][h]=newm[i][j];    nrfunc=func; 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    for (j=1;j<=n;j++) { 
          */      pcom[j]=p[j]; 
       }      xicom[j]=xi[j]; 
   } /* end h */    } 
   return po;    ax=0.0; 
 }    xx=1.0; 
     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 /*************** log-likelihood *************/  #ifdef DEBUG
 double func( double *x)    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 {    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   int i, ii, j, k, mi, d;  #endif
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    for (j=1;j<=n;j++) { 
   double **out;      xi[j] *= xmin; 
   double sw; /* Sum of weights */      p[j] += xi[j]; 
   double lli; /* Individual log likelihood */    } 
   long ipmx;    free_vector(xicom,1,n); 
   /*extern weight */    free_vector(pcom,1,n); 
   /* We are differentiating ll according to initial status */  } 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)  char *asc_diff_time(long time_sec, char ascdiff[])
 printf(" %d\n",s[4][i]);  {
   */    long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
   for(k=1; k<=nlstate; k++) ll[k]=0.;    sec_left = (time_sec) % (60*60*24);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    hours = (sec_left) / (60*60) ;
        for(mi=1; mi<= wav[i]-1; mi++){    sec_left = (sec_left) %(60*60);
       for (ii=1;ii<=nlstate+ndeath;ii++)    minutes = (sec_left) /60;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    sec_left = (sec_left) % (60);
             for(d=0; d<dh[mi][i]; d++){    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
         newm=savm;    return ascdiff;
           cov[1]=1.;  }
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
           if (cptcovn>0){  /*************** powell ************************/
             for (k=1; k<=cptcovn;k++) {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               cov[2+k]=covar[Tvar[k]][i];              double (*func)(double [])) 
               /* printf("k=%d cptcovn=%d %lf\n",k,cptcovn,covar[Tvar[k]][i]);*/  { 
             }    void linmin(double p[], double xi[], int n, double *fret, 
             }                double (*func)(double [])); 
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    int i,ibig,j; 
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    double del,t,*pt,*ptt,*xit;
           savm=oldm;    double fp,fptt;
           oldm=newm;    double *xits;
       } /* end mult */    int niterf, itmp;
      
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    pt=vector(1,n); 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    ptt=vector(1,n); 
       ipmx +=1;    xit=vector(1,n); 
       sw += weight[i];    xits=vector(1,n); 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    *fret=(*func)(p); 
     } /* end of wave */    for (j=1;j<=n;j++) pt[j]=p[j]; 
   } /* end of individual */    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      ibig=0; 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      del=0.0; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      last_time=curr_time;
       (void) gettimeofday(&curr_time,&tzp);
   return -l;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
 }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
       fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       for (i=1;i<=n;i++) {
 /*********** Maximum Likelihood Estimation ***************/        printf(" %d %.12f",i, p[i]);
         fprintf(ficlog," %d %.12lf",i, p[i]);
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        fprintf(ficrespow," %.12lf", p[i]);
 {      }
   int i,j, iter;      printf("\n");
   double **xi,*delti;      fprintf(ficlog,"\n");
   double fret;      fprintf(ficrespow,"\n");fflush(ficrespow);
   xi=matrix(1,npar,1,npar);      if(*iter <=3){
   for (i=1;i<=npar;i++)        tm = *localtime(&curr_time.tv_sec);
     for (j=1;j<=npar;j++)        strcpy(strcurr,asctime(&tmf));
       xi[i][j]=(i==j ? 1.0 : 0.0);  /*       asctime_r(&tm,strcurr); */
   printf("Powell\n");        forecast_time=curr_time;
   powell(p,xi,npar,ftol,&iter,&fret,func);        itmp = strlen(strcurr);
         if(strcurr[itmp-1]=='\n')
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          strcurr[itmp-1]='\0';
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
 }        for(niterf=10;niterf<=30;niterf+=10){
           forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
 /**** Computes Hessian and covariance matrix ***/          tmf = *localtime(&forecast_time.tv_sec);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  /*      asctime_r(&tmf,strfor); */
 {          strcpy(strfor,asctime(&tmf));
   double  **a,**y,*x,pd;          itmp = strlen(strfor);
   double **hess;          if(strfor[itmp-1]=='\n')
   int i, j,jk;          strfor[itmp-1]='\0';
   int *indx;          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
           fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
   double hessii(double p[], double delta, int theta, double delti[]);        }
   double hessij(double p[], double delti[], int i, int j);      }
   void lubksb(double **a, int npar, int *indx, double b[]) ;      for (i=1;i<=n;i++) { 
   void ludcmp(double **a, int npar, int *indx, double *d) ;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
   #ifdef DEBUG
   hess=matrix(1,npar,1,npar);        printf("fret=%lf \n",*fret);
         fprintf(ficlog,"fret=%lf \n",*fret);
   printf("\nCalculation of the hessian matrix. Wait...\n");  #endif
   for (i=1;i<=npar;i++){        printf("%d",i);fflush(stdout);
     printf("%d",i);fflush(stdout);        fprintf(ficlog,"%d",i);fflush(ficlog);
     hess[i][i]=hessii(p,ftolhess,i,delti);        linmin(p,xit,n,fret,func); 
     /*printf(" %f ",p[i]);*/        if (fabs(fptt-(*fret)) > del) { 
   }          del=fabs(fptt-(*fret)); 
           ibig=i; 
   for (i=1;i<=npar;i++) {        } 
     for (j=1;j<=npar;j++)  {  #ifdef DEBUG
       if (j>i) {        printf("%d %.12e",i,(*fret));
         printf(".%d%d",i,j);fflush(stdout);        fprintf(ficlog,"%d %.12e",i,(*fret));
         hess[i][j]=hessij(p,delti,i,j);        for (j=1;j<=n;j++) {
         hess[j][i]=hess[i][j];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       }          printf(" x(%d)=%.12e",j,xit[j]);
     }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   }        }
   printf("\n");        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          fprintf(ficlog," p=%.12e",p[j]);
          }
   a=matrix(1,npar,1,npar);        printf("\n");
   y=matrix(1,npar,1,npar);        fprintf(ficlog,"\n");
   x=vector(1,npar);  #endif
   indx=ivector(1,npar);      } 
   for (i=1;i<=npar;i++)      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  #ifdef DEBUG
   ludcmp(a,npar,indx,&pd);        int k[2],l;
         k[0]=1;
   for (j=1;j<=npar;j++) {        k[1]=-1;
     for (i=1;i<=npar;i++) x[i]=0;        printf("Max: %.12e",(*func)(p));
     x[j]=1;        fprintf(ficlog,"Max: %.12e",(*func)(p));
     lubksb(a,npar,indx,x);        for (j=1;j<=n;j++) {
     for (i=1;i<=npar;i++){          printf(" %.12e",p[j]);
       matcov[i][j]=x[i];          fprintf(ficlog," %.12e",p[j]);
     }        }
   }        printf("\n");
         fprintf(ficlog,"\n");
   printf("\n#Hessian matrix#\n");        for(l=0;l<=1;l++) {
   for (i=1;i<=npar;i++) {          for (j=1;j<=n;j++) {
     for (j=1;j<=npar;j++) {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       printf("%.3e ",hess[i][j]);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     printf("\n");          }
   }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   /* Recompute Inverse */        }
   for (i=1;i<=npar;i++)  #endif
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  
   ludcmp(a,npar,indx,&pd);  
         free_vector(xit,1,n); 
   /*  printf("\n#Hessian matrix recomputed#\n");        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
   for (j=1;j<=npar;j++) {        free_vector(pt,1,n); 
     for (i=1;i<=npar;i++) x[i]=0;        return; 
     x[j]=1;      } 
     lubksb(a,npar,indx,x);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     for (i=1;i<=npar;i++){      for (j=1;j<=n;j++) { 
       y[i][j]=x[i];        ptt[j]=2.0*p[j]-pt[j]; 
       printf("%.3e ",y[i][j]);        xit[j]=p[j]-pt[j]; 
     }        pt[j]=p[j]; 
     printf("\n");      } 
   }      fptt=(*func)(ptt); 
   */      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   free_matrix(a,1,npar,1,npar);        if (t < 0.0) { 
   free_matrix(y,1,npar,1,npar);          linmin(p,xit,n,fret,func); 
   free_vector(x,1,npar);          for (j=1;j<=n;j++) { 
   free_ivector(indx,1,npar);            xi[j][ibig]=xi[j][n]; 
   free_matrix(hess,1,npar,1,npar);            xi[j][n]=xit[j]; 
           }
   #ifdef DEBUG
 }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 /*************** hessian matrix ****************/          for(j=1;j<=n;j++){
 double hessii( double x[], double delta, int theta, double delti[])            printf(" %.12e",xit[j]);
 {            fprintf(ficlog," %.12e",xit[j]);
   int i;          }
   int l=1, lmax=20;          printf("\n");
   double k1,k2;          fprintf(ficlog,"\n");
   double p2[NPARMAX+1];  #endif
   double res;        }
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      } 
   double fx;    } 
   int k=0,kmax=10;  } 
   double l1;  
   /**** Prevalence limit (stable prevalence)  ****************/
   fx=func(x);  
   for (i=1;i<=npar;i++) p2[i]=x[i];  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   for(l=0 ; l <=lmax; l++){  {
     l1=pow(10,l);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     delts=delt;       matrix by transitions matrix until convergence is reached */
     for(k=1 ; k <kmax; k=k+1){  
       delt = delta*(l1*k);    int i, ii,j,k;
       p2[theta]=x[theta] +delt;    double min, max, maxmin, maxmax,sumnew=0.;
       k1=func(p2)-fx;    double **matprod2();
       p2[theta]=x[theta]-delt;    double **out, cov[NCOVMAX], **pmij();
       k2=func(p2)-fx;    double **newm;
       /*res= (k1-2.0*fx+k2)/delt/delt; */    double agefin, delaymax=50 ; /* Max number of years to converge */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  
          for (ii=1;ii<=nlstate+ndeath;ii++)
 #ifdef DEBUG      for (j=1;j<=nlstate+ndeath;j++){
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 #endif      }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){     cov[1]=1.;
         k=kmax;   
       }   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
         k=kmax; l=lmax*10.;      newm=savm;
       }      /* Covariates have to be included here again */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){       cov[2]=agefin;
         delts=delt;    
       }        for (k=1; k<=cptcovn;k++) {
     }          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]]);*/
   delti[theta]=delts;        }
   return res;          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]]];
 double hessij( double x[], double delti[], int thetai,int thetaj)  
 {        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   int i;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   int l=1, l1, lmax=20;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   double k1,k2,k3,k4,res,fx;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   double p2[NPARMAX+1];  
   int k;      savm=oldm;
       oldm=newm;
   fx=func(x);      maxmax=0.;
   for (k=1; k<=2; k++) {      for(j=1;j<=nlstate;j++){
     for (i=1;i<=npar;i++) p2[i]=x[i];        min=1.;
     p2[thetai]=x[thetai]+delti[thetai]/k;        max=0.;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        for(i=1; i<=nlstate; i++) {
     k1=func(p2)-fx;          sumnew=0;
            for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     p2[thetai]=x[thetai]+delti[thetai]/k;          prlim[i][j]= newm[i][j]/(1-sumnew);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          max=FMAX(max,prlim[i][j]);
     k2=func(p2)-fx;          min=FMIN(min,prlim[i][j]);
          }
     p2[thetai]=x[thetai]-delti[thetai]/k;        maxmin=max-min;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        maxmax=FMAX(maxmax,maxmin);
     k3=func(p2)-fx;      }
        if(maxmax < ftolpl){
     p2[thetai]=x[thetai]-delti[thetai]/k;        return prlim;
     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 */  }
 #ifdef DEBUG  
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  /*************** transition probabilities ***************/ 
 #endif  
   }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   return res;  {
 }    double s1, s2;
     /*double t34;*/
 /************** Inverse of matrix **************/    int i,j,j1, nc, ii, jj;
 void ludcmp(double **a, int n, int *indx, double *d)  
 {      for(i=1; i<= nlstate; i++){
   int i,imax,j,k;      for(j=1; j<i;j++){
   double big,dum,sum,temp;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   double *vv;          /*s2 += param[i][j][nc]*cov[nc];*/
            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   vv=vector(1,n);          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
   *d=1.0;        }
   for (i=1;i<=n;i++) {        ps[i][j]=s2;
     big=0.0;        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
     for (j=1;j<=n;j++)      }
       if ((temp=fabs(a[i][j])) > big) big=temp;      for(j=i+1; j<=nlstate+ndeath;j++){
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     vv[i]=1.0/big;          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   }          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   for (j=1;j<=n;j++) {        }
     for (i=1;i<j;i++) {        ps[i][j]=s2;
       sum=a[i][j];      }
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    }
       a[i][j]=sum;      /*ps[3][2]=1;*/
     }  
     big=0.0;    for(i=1; i<= nlstate; i++){
     for (i=j;i<=n;i++) {       s1=0;
       sum=a[i][j];      for(j=1; j<i; j++)
       for (k=1;k<j;k++)        s1+=exp(ps[i][j]);
         sum -= a[i][k]*a[k][j];      for(j=i+1; j<=nlstate+ndeath; j++)
       a[i][j]=sum;        s1+=exp(ps[i][j]);
       if ( (dum=vv[i]*fabs(sum)) >= big) {      ps[i][i]=1./(s1+1.);
         big=dum;      for(j=1; j<i; j++)
         imax=i;        ps[i][j]= exp(ps[i][j])*ps[i][i];
       }      for(j=i+1; j<=nlstate+ndeath; j++)
     }        ps[i][j]= exp(ps[i][j])*ps[i][i];
     if (j != imax) {      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       for (k=1;k<=n;k++) {    } /* end i */
         dum=a[imax][k];  
         a[imax][k]=a[j][k];    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         a[j][k]=dum;      for(jj=1; jj<= nlstate+ndeath; jj++){
       }        ps[ii][jj]=0;
       *d = -(*d);        ps[ii][ii]=1;
       vv[imax]=vv[j];      }
     }    }
     indx[j]=imax;  
     if (a[j][j] == 0.0) a[j][j]=TINY;  
     if (j != n) {    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
       dum=1.0/(a[j][j]);      for(jj=1; jj<= nlstate+ndeath; jj++){
       for (i=j+1;i<=n;i++) a[i][j] *= dum;       printf("%lf ",ps[ii][jj]);
     }     }
   }      printf("\n ");
   free_vector(vv,1,n);  /* Doesn't work */      }
 ;      printf("\n ");printf("%lf ",cov[2]);*/
 }  /*
     for(i=1; i<= npar; i++) printf("%f ",x[i]);
 void lubksb(double **a, int n, int *indx, double b[])    goto end;*/
 {      return ps;
   int i,ii=0,ip,j;  }
   double sum;  
    /**************** Product of 2 matrices ******************/
   for (i=1;i<=n;i++) {  
     ip=indx[i];  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     sum=b[ip];  {
     b[ip]=b[i];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     if (ii)       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    /* in, b, out are matrice of pointers which should have been initialized 
     else if (sum) ii=i;       before: only the contents of out is modified. The function returns
     b[i]=sum;       a pointer to pointers identical to out */
   }    long i, j, k;
   for (i=n;i>=1;i--) {    for(i=nrl; i<= nrh; i++)
     sum=b[i];      for(k=ncolol; k<=ncoloh; k++)
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     b[i]=sum/a[i][i];          out[i][k] +=in[i][j]*b[j][k];
   }  
 }    return out;
   }
 /************ Frequencies ********************/  
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)  
 {  /* Some frequencies */  /************* Higher Matrix Product ***************/
    
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   double ***freq; /* Frequencies */  {
   double *pp;    /* Computes the transition matrix starting at age 'age' over 
   double pos;       'nhstepm*hstepm*stepm' months (i.e. until
   FILE *ficresp;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   char fileresp[FILENAMELENGTH];       nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   pp=vector(1,nlstate);       (typically every 2 years instead of every month which is too big 
        for the memory).
   strcpy(fileresp,"p");       Model is determined by parameters x and covariates have to be 
   strcat(fileresp,fileres);       included manually here. 
   if((ficresp=fopen(fileresp,"w"))==NULL) {  
     printf("Problem with prevalence resultfile: %s\n", fileresp);       */
     exit(0);  
   }    int i, j, d, h, k;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    double **out, cov[NCOVMAX];
   j1=0;    double **newm;
   
   j=cptcovn;    /* Hstepm could be zero and should return the unit matrix */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
   for(k1=1; k1<=j;k1++){        oldm[i][j]=(i==j ? 1.0 : 0.0);
    for(i1=1; i1<=ncodemax[k1];i1++){        po[i][j][0]=(i==j ? 1.0 : 0.0);
        j1++;      }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         for (i=-1; i<=nlstate+ndeath; i++)      for(h=1; h <=nhstepm; h++){
          for (jk=-1; jk<=nlstate+ndeath; jk++)        for(d=1; d <=hstepm; d++){
            for(m=agemin; m <= agemax+3; m++)        newm=savm;
              freq[i][jk][m]=0;        /* Covariates have to be included here again */
                cov[1]=1.;
        for (i=1; i<=imx; i++) {        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
          bool=1;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
          if  (cptcovn>0) {        for (k=1; k<=cptcovage;k++)
            for (z1=1; z1<=cptcovn; z1++)          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;        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]]];
           if (bool==1) {  
            for(m=firstpass; m<=lastpass-1; m++){  
              if(agev[m][i]==0) agev[m][i]=agemax+1;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
              if(agev[m][i]==1) agev[m][i]=agemax+2;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];                     pmij(pmmij,cov,ncovmodel,x,nlstate));
            }        savm=oldm;
          }        oldm=newm;
        }      }
         if  (cptcovn>0) {      for(i=1; i<=nlstate+ndeath; i++)
          fprintf(ficresp, "\n#Variable");        for(j=1;j<=nlstate+ndeath;j++) {
          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);          po[i][j][h]=newm[i][j];
        }          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
        fprintf(ficresp, "\n#");           */
        for(i=1; i<=nlstate;i++)        }
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    } /* end h */
        fprintf(ficresp, "\n");    return po;
          }
   for(i=(int)agemin; i <= (int)agemax+3; i++){  
     if(i==(int)agemax+3)  
       printf("Total");  /*************** log-likelihood *************/
     else  double func( double *x)
       printf("Age %d", i);  {
     for(jk=1; jk <=nlstate ; jk++){    int i, ii, j, k, mi, d, kk;
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         pp[jk] += freq[jk][m][i];    double **out;
     }    double sw; /* Sum of weights */
     for(jk=1; jk <=nlstate ; jk++){    double lli; /* Individual log likelihood */
       for(m=-1, pos=0; m <=0 ; m++)    int s1, s2;
         pos += freq[jk][m][i];    double bbh, survp;
       if(pp[jk]>=1.e-10)    long ipmx;
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    /*extern weight */
       else    /* We are differentiating ll according to initial status */
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     }    /*for(i=1;i<imx;i++) 
     for(jk=1; jk <=nlstate ; jk++){      printf(" %d\n",s[4][i]);
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)    */
         pp[jk] += freq[jk][m][i];    cov[1]=1.;
     }  
     for(jk=1,pos=0; jk <=nlstate ; jk++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
       pos += pp[jk];  
     for(jk=1; jk <=nlstate ; jk++){    if(mle==1){
       if(pos>=1.e-5)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       else        for(mi=1; mi<= wav[i]-1; mi++){
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          for (ii=1;ii<=nlstate+ndeath;ii++)
       if( i <= (int) agemax){            for (j=1;j<=nlstate+ndeath;j++){
         if(pos>=1.e-5)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       else            }
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          for(d=0; d<dh[mi][i]; d++){
       }            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(jk=-1; jk <=nlstate+ndeath; jk++)            for (kk=1; kk<=cptcovage;kk++) {
       for(m=-1; m <=nlstate+ndeath; m++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            }
     if(i <= (int) agemax)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       fprintf(ficresp,"\n");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     printf("\n");            savm=oldm;
     }            oldm=newm;
     }          } /* end mult */
  }        
            /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   fclose(ficresp);          /* But now since version 0.9 we anticipate for bias and large stepm.
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   free_vector(pp,1,nlstate);           * (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
 }  /* End of Freq */           * 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'. The we inter(extra)polate the
 /************* Waves Concatenation ***************/           * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)           * -stepm/2 to stepm/2 .
 {           * For stepm=1 the results are the same as for previous versions of Imach.
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.           * For stepm > 1 the results are less biased than in previous versions. 
      Death is a valid wave (if date is known).           */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          s1=s[mw[mi][i]][i];
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          s2=s[mw[mi+1][i]][i];
      and mw[mi+1][i]. dh depends on stepm.          bbh=(double)bh[mi][i]/(double)stepm; 
      */          /* bias is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
   int i, mi, m;           */
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 float sum=0.;          if( s2 > nlstate){ 
             /* i.e. if s2 is a death state and if the date of death is known then the contribution
   for(i=1; i<=imx; i++){               to the likelihood is the probability to die between last step unit time and current 
     mi=0;               step unit time, which is also the differences between probability to die before dh 
     m=firstpass;               and probability to die before dh-stepm . 
     while(s[m][i] <= nlstate){               In version up to 0.92 likelihood was computed
       if(s[m][i]>=1)          as if date of death was unknown. Death was treated as any other
         mw[++mi][i]=m;          health state: the date of the interview describes the actual state
       if(m >=lastpass)          and not the date of a change in health state. The former idea was
         break;          to consider that at each interview the state was recorded
       else          (healthy, disable or death) and IMaCh was corrected; but when we
         m++;          introduced the exact date of death then we should have modified
     }/* end while */          the contribution of an exact death to the likelihood. This new
     if (s[m][i] > nlstate){          contribution is smaller and very dependent of the step unit
       mi++;     /* Death is another wave */          stepm. It is no more the probability to die between last interview
       /* if(mi==0)  never been interviewed correctly before death */          and month of death but the probability to survive from last
          /* Only death is a correct wave */          interview up to one month before death multiplied by the
       mw[mi][i]=m;          probability to die within a month. Thanks to Chris
     }          Jackson for correcting this bug.  Former versions increased
           mortality artificially. The bad side is that we add another loop
     wav[i]=mi;          which slows down the processing. The difference can be up to 10%
     if(mi==0)          lower mortality.
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            */
   }            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
   for(i=1; i<=imx; i++){            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     for(mi=1; mi<wav[i];mi++){            /*  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 */
       if (stepm <=0)          } 
         dh[mi][i]=1;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       else{          /*if(lli ==000.0)*/
         if (s[mw[mi+1][i]][i] > nlstate) {          /*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); */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          ipmx +=1;
           if(j=0) j=1;  /* Survives at least one month after exam */          sw += weight[i];
         }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         else{        } /* end of wave */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      } /* end of individual */
           /*printf("i=%d agevi+1=%lf agevi=%lf j=%d\n", i,agev[mw[mi+1][i]][i],agev[mw[mi][i]][i],j);*/    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           k=k+1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           if (j >= jmax) jmax=j;        for(mi=1; mi<= wav[i]-1; mi++){
           else if (j <= jmin)jmin=j;          for (ii=1;ii<=nlstate+ndeath;ii++)
           sum=sum+j;            for (j=1;j<=nlstate+ndeath;j++){
         }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         jk= j/stepm;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         jl= j -jk*stepm;            }
         ju= j -(jk+1)*stepm;          for(d=0; d<=dh[mi][i]; d++){
         if(jl <= -ju)            newm=savm;
           dh[mi][i]=jk;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         else            for (kk=1; kk<=cptcovage;kk++) {
           dh[mi][i]=jk+1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         if(dh[mi][i]==0)            }
           dh[mi][i]=1; /* At least one step */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
   }            oldm=newm;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);          } /* end mult */
 }        
 /*********** Tricode ****************************/          s1=s[mw[mi][i]][i];
 void tricode(int *Tvar, int **nbcode, int imx)          s2=s[mw[mi+1][i]][i];
 {          bbh=(double)bh[mi][i]/(double)stepm; 
   int Ndum[80],ij, k, j, i;          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 cptcode=0;          ipmx +=1;
   for (k=0; k<79; k++) Ndum[k]=0;          sw += weight[i];
   for (k=1; k<=7; k++) ncodemax[k]=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
   for (j=1; j<=cptcovn; j++) {      } /* end of individual */
     for (i=1; i<=imx; i++) {    }  else if(mle==3){  /* exponential inter-extrapolation */
       ij=(int)(covar[Tvar[j]][i]);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       Ndum[ij]++;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       if (ij > cptcode) cptcode=ij;        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/            for (j=1;j<=nlstate+ndeath;j++){
     for (i=0; i<=cptcode; i++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       if(Ndum[i]!=0) ncodemax[j]++;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }            }
            for(d=0; d<dh[mi][i]; d++){
     ij=1;            newm=savm;
     for (i=1; i<=ncodemax[j]; i++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for (k=0; k<=79; k++) {            for (kk=1; kk<=cptcovage;kk++) {
         if (Ndum[k] != 0) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           nbcode[Tvar[j]][ij]=k;            }
           ij++;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if (ij > ncodemax[j]) break;            savm=oldm;
       }              oldm=newm;
     }          } /* end mult */
   }          
           s1=s[mw[mi][i]][i];
   }          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
 /*********** Health Expectancies ****************/          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
           ipmx +=1;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* Health expectancies */        } /* end of wave */
   int i, j, nhstepm, hstepm, h;      } /* end of individual */
   double age, agelim,hf;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   double ***p3mat;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fprintf(ficreseij,"# Health expectancies\n");        for(mi=1; mi<= wav[i]-1; mi++){
   fprintf(ficreseij,"# Age");          for (ii=1;ii<=nlstate+ndeath;ii++)
   for(i=1; i<=nlstate;i++)            for (j=1;j<=nlstate+ndeath;j++){
     for(j=1; j<=nlstate;j++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficreseij," %1d-%1d",i,j);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficreseij,"\n");            }
           for(d=0; d<dh[mi][i]; d++){
   hstepm=1*YEARM; /*  Every j years of age (in month) */            newm=savm;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             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 age range expressed in number of stepm */          
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     /* Typically if 20 years = 20*12/6=40 stepm */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     if (stepm >= YEARM) hstepm=1;            savm=oldm;
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */            oldm=newm;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          } /* end mult */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          s1=s[mw[mi][i]][i];
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            s2=s[mw[mi+1][i]][i];
           if( s2 > nlstate){ 
             lli=log(out[s1][s2] - savm[s1][s2]);
     for(i=1; i<=nlstate;i++)          }else{
       for(j=1; j<=nlstate;j++)            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          }
           eij[i][j][(int)age] +=p3mat[i][j][h];          ipmx +=1;
         }          sw += weight[i];
              ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     hf=1;  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     if (stepm >= YEARM) hf=stepm/YEARM;        } /* end of wave */
     fprintf(ficreseij,"%.0f",age );      } /* end of individual */
     for(i=1; i<=nlstate;i++)    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for(j=1; j<=nlstate;j++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       }        for(mi=1; mi<= wav[i]-1; mi++){
     fprintf(ficreseij,"\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
 /************ Variance ******************/          for(d=0; d<dh[mi][i]; d++){
 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)            newm=savm;
 {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /* Variance of health expectancies */            for (kk=1; kk<=cptcovage;kk++) {
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double **newm;            }
   double **dnewm,**doldm;          
   int i, j, nhstepm, hstepm, h;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int k, cptcode;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
    double *xp;            savm=oldm;
   double **gp, **gm;            oldm=newm;
   double ***gradg, ***trgradg;          } /* end mult */
   double ***p3mat;        
   double age,agelim;          s1=s[mw[mi][i]][i];
   int theta;          s2=s[mw[mi+1][i]][i];
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
    fprintf(ficresvij,"# Covariances of life expectancies\n");          ipmx +=1;
   fprintf(ficresvij,"# Age");          sw += weight[i];
   for(i=1; i<=nlstate;i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(j=1; j<=nlstate;j++)          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        } /* end of wave */
   fprintf(ficresvij,"\n");      } /* end of individual */
     } /* End of if */
   xp=vector(1,npar);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   dnewm=matrix(1,nlstate,1,npar);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   doldm=matrix(1,nlstate,1,nlstate);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      return -l;
   hstepm=1*YEARM; /* Every year of age */  }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   agelim = AGESUP;  /*************** log-likelihood *************/
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  double funcone( double *x)
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  {
     if (stepm >= YEARM) hstepm=1;    /* Same as likeli but slower because of a lot of printf and if */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    int i, ii, j, k, mi, d, kk;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    double **out;
     gp=matrix(0,nhstepm,1,nlstate);    double lli; /* Individual log likelihood */
     gm=matrix(0,nhstepm,1,nlstate);    double llt;
     int s1, s2;
     for(theta=1; theta <=npar; theta++){    double bbh, survp;
       for(i=1; i<=npar; i++){ /* Computes gradient */    /*extern weight */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    /* We are differentiating ll according to initial status */
       }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      /*for(i=1;i<imx;i++) 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      printf(" %d\n",s[4][i]);
       for(j=1; j<= nlstate; j++){    */
         for(h=0; h<=nhstepm; h++){    cov[1]=1.;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    for(k=1; k<=nlstate; k++) ll[k]=0.;
         }  
       }    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(i=1; i<=npar; i++) /* Computes gradient */      for(mi=1; mi<= wav[i]-1; mi++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        for (ii=1;ii<=nlstate+ndeath;ii++)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            for (j=1;j<=nlstate+ndeath;j++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<= nlstate; j++){            savm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(h=0; h<=nhstepm; h++){          }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        for(d=0; d<dh[mi][i]; d++){
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          newm=savm;
         }          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }          for (kk=1; kk<=cptcovage;kk++) {
       for(j=1; j<= nlstate; j++)            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for(h=0; h<=nhstepm; h++){          }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     } /* End theta */          savm=oldm;
           oldm=newm;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        } /* end mult */
         
     for(h=0; h<=nhstepm; h++)        s1=s[mw[mi][i]][i];
       for(j=1; j<=nlstate;j++)        s2=s[mw[mi+1][i]][i];
         for(theta=1; theta <=npar; theta++)        bbh=(double)bh[mi][i]/(double)stepm; 
           trgradg[h][j][theta]=gradg[h][theta][j];        /* bias is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.
     for(i=1;i<=nlstate;i++)         */
       for(j=1;j<=nlstate;j++)        if( s2 > nlstate && (mle <5) ){  /* Jackson */
         vareij[i][j][(int)age] =0.;          lli=log(out[s1][s2] - savm[s1][s2]);
     for(h=0;h<=nhstepm;h++){        } else if (mle==1){
       for(k=0;k<=nhstepm;k++){          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        } else if(mle==2){
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         for(i=1;i<=nlstate;i++)        } else if(mle==3){  /* exponential inter-extrapolation */
           for(j=1;j<=nlstate;j++)          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 */
             vareij[i][j][(int)age] += doldm[i][j];        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       }          lli=log(out[s1][s2]); /* Original formula */
     }        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
     h=1;          lli=log(out[s1][s2]); /* Original formula */
     if (stepm >= YEARM) h=stepm/YEARM;        } /* End of if */
     fprintf(ficresvij,"%.0f ",age );        ipmx +=1;
     for(i=1; i<=nlstate;i++)        sw += weight[i];
       for(j=1; j<=nlstate;j++){        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);  /*       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]); */
       }        if(globpr){
     fprintf(ficresvij,"\n");          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
     free_matrix(gp,0,nhstepm,1,nlstate);   %10.6f %10.6f %10.6f ", \
     free_matrix(gm,0,nhstepm,1,nlstate);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            llt +=ll[k]*gipmx/gsw;
   } /* End age */            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
            }
   free_vector(xp,1,npar);          fprintf(ficresilk," %10.6f\n", -llt);
   free_matrix(doldm,1,nlstate,1,npar);        }
   free_matrix(dnewm,1,nlstate,1,nlstate);      } /* end of wave */
     } /* end of individual */
 }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
 /************ Variance of prevlim ******************/    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
 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)    if(globpr==0){ /* First time we count the contributions and weights */
 {      gipmx=ipmx;
   /* Variance of prevalence limit */      gsw=sw;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    }
   double **newm;    return -l;
   double **dnewm,**doldm;  }
   int i, j, nhstepm, hstepm;  
   int k, cptcode;  
   double *xp;  /*************** function likelione ***********/
   double *gp, *gm;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   double **gradg, **trgradg;  {
   double age,agelim;    /* This routine should help understanding what is done with 
   int theta;       the selection of individuals/waves and
           to check the exact contribution to the likelihood.
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");       Plotting could be done.
   fprintf(ficresvpl,"# Age");     */
   for(i=1; i<=nlstate;i++)    int k;
       fprintf(ficresvpl," %1d-%1d",i,i);  
   fprintf(ficresvpl,"\n");    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
   xp=vector(1,npar);      strcat(fileresilk,fileres);
   dnewm=matrix(1,nlstate,1,npar);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   doldm=matrix(1,nlstate,1,nlstate);        printf("Problem with resultfile: %s\n", fileresilk);
          fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   hstepm=1*YEARM; /* Every year of age */      }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      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");
   agelim = AGESUP;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      for(k=1; k<=nlstate; k++) 
     if (stepm >= YEARM) hstepm=1;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     gradg=matrix(1,npar,1,nlstate);    }
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);    *fretone=(*funcone)(p);
     if(*globpri !=0){
     for(theta=1; theta <=npar; theta++){      fclose(ficresilk);
       for(i=1; i<=npar; i++){ /* Computes gradient */      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      fflush(fichtm); 
       }    } 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    return;
       for(i=1;i<=nlstate;i++)  }
         gp[i] = prlim[i][i];  
      
       for(i=1; i<=npar; i++) /* Computes gradient */  /*********** Maximum Likelihood Estimation ***************/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       for(i=1;i<=nlstate;i++)  {
         gm[i] = prlim[i][i];    int i,j, iter;
     double **xi;
       for(i=1;i<=nlstate;i++)    double fret;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    double fretone; /* Only one call to likelihood */
     } /* End theta */    char filerespow[FILENAMELENGTH];
     xi=matrix(1,npar,1,npar);
     trgradg =matrix(1,nlstate,1,npar);    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
     for(j=1; j<=nlstate;j++)        xi[i][j]=(i==j ? 1.0 : 0.0);
       for(theta=1; theta <=npar; theta++)    printf("Powell\n");  fprintf(ficlog,"Powell\n");
         trgradg[j][theta]=gradg[theta][j];    strcpy(filerespow,"pow"); 
     strcat(filerespow,fileres);
     for(i=1;i<=nlstate;i++)    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       varpl[i][(int)age] =0.;      printf("Problem with resultfile: %s\n", filerespow);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    }
     for(i=1;i<=nlstate;i++)    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
     fprintf(ficresvpl,"%.0f ",age );        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     for(i=1; i<=nlstate;i++)    fprintf(ficrespow,"\n");
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  
     fprintf(ficresvpl,"\n");    powell(p,xi,npar,ftol,&iter,&fret,func);
     free_vector(gp,1,nlstate);  
     free_vector(gm,1,nlstate);    fclose(ficrespow);
     free_matrix(gradg,1,npar,1,nlstate);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     free_matrix(trgradg,1,nlstate,1,npar);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   } /* End age */    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   
   free_vector(xp,1,npar);  }
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);  /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
 }  {
     double  **a,**y,*x,pd;
     double **hess;
     int i, j,jk;
 /***********************************************/    int *indx;
 /**************** Main Program *****************/  
 /***********************************************/    double hessii(double p[], double delta, int theta, double delti[]);
     double hessij(double p[], double delti[], int i, int j);
 /*int main(int argc, char *argv[])*/    void lubksb(double **a, int npar, int *indx, double b[]) ;
 int main()    void ludcmp(double **a, int npar, int *indx, double *d) ;
 {  
     hess=matrix(1,npar,1,npar);
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;  
   double agedeb, agefin,hf;    printf("\nCalculation of the hessian matrix. Wait...\n");
   double agemin=1.e20, agemax=-1.e20;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
   double fret;      printf("%d",i);fflush(stdout);
   double **xi,tmp,delta;      fprintf(ficlog,"%d",i);fflush(ficlog);
       hess[i][i]=hessii(p,ftolhess,i,delti);
   double dum; /* Dummy variable */      /*printf(" %f ",p[i]);*/
   double ***p3mat;      /*printf(" %lf ",hess[i][i]);*/
   int *indx;    }
   char line[MAXLINE], linepar[MAXLINE];    
   char title[MAXLINE];    for (i=1;i<=npar;i++) {
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      for (j=1;j<=npar;j++)  {
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];        if (j>i) { 
   char filerest[FILENAMELENGTH];          printf(".%d%d",i,j);fflush(stdout);
   char fileregp[FILENAMELENGTH];          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          hess[i][j]=hessij(p,delti,i,j);
   int firstobs=1, lastobs=10;          hess[j][i]=hess[i][j];    
   int sdeb, sfin; /* Status at beginning and end */          /*printf(" %lf ",hess[i][j]);*/
   int c,  h , cpt,l;        }
   int ju,jl, mi;      }
   int i1,j1, k1,jk,aa,bb, stepsize;    }
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    printf("\n");
      fprintf(ficlog,"\n");
   int hstepm, nhstepm;  
   double bage, fage, age, agelim, agebase;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   double ftolpl=FTOL;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   double **prlim;    
   double *severity;    a=matrix(1,npar,1,npar);
   double ***param; /* Matrix of parameters */    y=matrix(1,npar,1,npar);
   double  *p;    x=vector(1,npar);
   double **matcov; /* Matrix of covariance */    indx=ivector(1,npar);
   double ***delti3; /* Scale */    for (i=1;i<=npar;i++)
   double *delti; /* Scale */      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   double ***eij, ***vareij;    ludcmp(a,npar,indx,&pd);
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;    for (j=1;j<=npar;j++) {
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";      for (i=1;i<=npar;i++) x[i]=0;
   char *alph[]={"a","a","b","c","d","e"}, str[4];      x[j]=1;
   char z[1]="c", occ;      lubksb(a,npar,indx,x);
 #include <sys/time.h>      for (i=1;i<=npar;i++){ 
 #include <time.h>        matcov[i][j]=x[i];
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      }
   /* long total_usecs;    }
   struct timeval start_time, end_time;  
      printf("\n#Hessian matrix#\n");
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
   printf("\nIMACH, Version 0.63");        printf("%.3e ",hess[i][j]);
   printf("\nEnter the parameter file name: ");        fprintf(ficlog,"%.3e ",hess[i][j]);
       }
 #ifdef windows      printf("\n");
   scanf("%s",pathtot);      fprintf(ficlog,"\n");
   getcwd(pathcd, size);    }
   cutv(path,optionfile,pathtot,'\\');  
   chdir(path);    /* Recompute Inverse */
   replace(pathc,path);    for (i=1;i<=npar;i++)
 #endif      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
 #ifdef unix    ludcmp(a,npar,indx,&pd);
   scanf("%s",optionfile);  
 #endif    /*  printf("\n#Hessian matrix recomputed#\n");
   
 /*-------- arguments in the command line --------*/    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
   strcpy(fileres,"r");      x[j]=1;
   strcat(fileres, optionfile);      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
   /*---------arguments file --------*/        y[i][j]=x[i];
         printf("%.3e ",y[i][j]);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        fprintf(ficlog,"%.3e ",y[i][j]);
     printf("Problem with optionfile %s\n",optionfile);      }
     goto end;      printf("\n");
   }      fprintf(ficlog,"\n");
     }
   strcpy(filereso,"o");    */
   strcat(filereso,fileres);  
   if((ficparo=fopen(filereso,"w"))==NULL) {    free_matrix(a,1,npar,1,npar);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    free_matrix(y,1,npar,1,npar);
   }    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
   /* Reads comments: lines beginning with '#' */    free_matrix(hess,1,npar,1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  }
     puts(line);  
     fputs(line,ficparo);  /*************** hessian matrix ****************/
   }  double hessii( double x[], double delta, int theta, double delti[])
   ungetc(c,ficpar);  {
     int i;
   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);    int l=1, lmax=20;
   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);    double k1,k2;
   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);    double p2[NPARMAX+1];
     double res;
   covar=matrix(1,NCOVMAX,1,n);        double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   if (strlen(model)<=1) cptcovn=0;    double fx;
   else {    int k=0,kmax=10;
     j=0;    double l1;
     j=nbocc(model,'+');  
     cptcovn=j+1;    fx=func(x);
   }    for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){
   ncovmodel=2+cptcovn;      l1=pow(10,l);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      delts=delt;
        for(k=1 ; k <kmax; k=k+1){
   /* Read guess parameters */        delt = delta*(l1*k);
   /* Reads comments: lines beginning with '#' */        p2[theta]=x[theta] +delt;
   while((c=getc(ficpar))=='#' && c!= EOF){        k1=func(p2)-fx;
     ungetc(c,ficpar);        p2[theta]=x[theta]-delt;
     fgets(line, MAXLINE, ficpar);        k2=func(p2)-fx;
     puts(line);        /*res= (k1-2.0*fx+k2)/delt/delt; */
     fputs(line,ficparo);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   }        
   ungetc(c,ficpar);  #ifdef DEBUG
          printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        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);
     for(i=1; i <=nlstate; i++)  #endif
     for(j=1; j <=nlstate+ndeath-1; j++){        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       fscanf(ficpar,"%1d%1d",&i1,&j1);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       fprintf(ficparo,"%1d%1d",i1,j1);          k=kmax;
       printf("%1d%1d",i,j);        }
       for(k=1; k<=ncovmodel;k++){        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         fscanf(ficpar," %lf",&param[i][j][k]);          k=kmax; l=lmax*10.;
         printf(" %lf",param[i][j][k]);        }
         fprintf(ficparo," %lf",param[i][j][k]);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       }          delts=delt;
       fscanf(ficpar,"\n");        }
       printf("\n");      }
       fprintf(ficparo,"\n");    }
     }    delti[theta]=delts;
      return res; 
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    
   p=param[1][1];  }
    
   /* Reads comments: lines beginning with '#' */  double hessij( double x[], double delti[], int thetai,int thetaj)
   while((c=getc(ficpar))=='#' && c!= EOF){  {
     ungetc(c,ficpar);    int i;
     fgets(line, MAXLINE, ficpar);    int l=1, l1, lmax=20;
     puts(line);    double k1,k2,k3,k4,res,fx;
     fputs(line,ficparo);    double p2[NPARMAX+1];
   }    int k;
   ungetc(c,ficpar);  
     fx=func(x);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    for (k=1; k<=2; k++) {
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      for (i=1;i<=npar;i++) p2[i]=x[i];
   for(i=1; i <=nlstate; i++){      p2[thetai]=x[thetai]+delti[thetai]/k;
     for(j=1; j <=nlstate+ndeath-1; j++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       fscanf(ficpar,"%1d%1d",&i1,&j1);      k1=func(p2)-fx;
       printf("%1d%1d",i,j);    
       fprintf(ficparo,"%1d%1d",i1,j1);      p2[thetai]=x[thetai]+delti[thetai]/k;
       for(k=1; k<=ncovmodel;k++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         fscanf(ficpar,"%le",&delti3[i][j][k]);      k2=func(p2)-fx;
         printf(" %le",delti3[i][j][k]);    
         fprintf(ficparo," %le",delti3[i][j][k]);      p2[thetai]=x[thetai]-delti[thetai]/k;
       }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       fscanf(ficpar,"\n");      k3=func(p2)-fx;
       printf("\n");    
       fprintf(ficparo,"\n");      p2[thetai]=x[thetai]-delti[thetai]/k;
     }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   }      k4=func(p2)-fx;
   delti=delti3[1][1];      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
    #ifdef DEBUG
   /* Reads comments: lines beginning with '#' */      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);
   while((c=getc(ficpar))=='#' && c!= EOF){      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);
     ungetc(c,ficpar);  #endif
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    return res;
     fputs(line,ficparo);  }
   }  
   ungetc(c,ficpar);  /************** Inverse of matrix **************/
    void ludcmp(double **a, int n, int *indx, double *d) 
   matcov=matrix(1,npar,1,npar);  { 
   for(i=1; i <=npar; i++){    int i,imax,j,k; 
     fscanf(ficpar,"%s",&str);    double big,dum,sum,temp; 
     printf("%s",str);    double *vv; 
     fprintf(ficparo,"%s",str);   
     for(j=1; j <=i; j++){    vv=vector(1,n); 
       fscanf(ficpar," %le",&matcov[i][j]);    *d=1.0; 
       printf(" %.5le",matcov[i][j]);    for (i=1;i<=n;i++) { 
       fprintf(ficparo," %.5le",matcov[i][j]);      big=0.0; 
     }      for (j=1;j<=n;j++) 
     fscanf(ficpar,"\n");        if ((temp=fabs(a[i][j])) > big) big=temp; 
     printf("\n");      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     fprintf(ficparo,"\n");      vv[i]=1.0/big; 
   }    } 
   for(i=1; i <=npar; i++)    for (j=1;j<=n;j++) { 
     for(j=i+1;j<=npar;j++)      for (i=1;i<j;i++) { 
       matcov[i][j]=matcov[j][i];        sum=a[i][j]; 
            for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   printf("\n");        a[i][j]=sum; 
       } 
       big=0.0; 
    if(mle==1){      for (i=j;i<=n;i++) { 
     /*-------- data file ----------*/        sum=a[i][j]; 
     if((ficres =fopen(fileres,"w"))==NULL) {        for (k=1;k<j;k++) 
       printf("Problem with resultfile: %s\n", fileres);goto end;          sum -= a[i][k]*a[k][j]; 
     }        a[i][j]=sum; 
     fprintf(ficres,"#%s\n",version);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
              big=dum; 
     if((fic=fopen(datafile,"r"))==NULL)    {          imax=i; 
       printf("Problem with datafile: %s\n", datafile);goto end;        } 
     }      } 
       if (j != imax) { 
     n= lastobs;        for (k=1;k<=n;k++) { 
     severity = vector(1,maxwav);          dum=a[imax][k]; 
     outcome=imatrix(1,maxwav+1,1,n);          a[imax][k]=a[j][k]; 
     num=ivector(1,n);          a[j][k]=dum; 
     moisnais=vector(1,n);        } 
     annais=vector(1,n);        *d = -(*d); 
     moisdc=vector(1,n);        vv[imax]=vv[j]; 
     andc=vector(1,n);      } 
     agedc=vector(1,n);      indx[j]=imax; 
     cod=ivector(1,n);      if (a[j][j] == 0.0) a[j][j]=TINY; 
     weight=vector(1,n);      if (j != n) { 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        dum=1.0/(a[j][j]); 
     mint=matrix(1,maxwav,1,n);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     anint=matrix(1,maxwav,1,n);      } 
     s=imatrix(1,maxwav+1,1,n);    } 
     adl=imatrix(1,maxwav+1,1,n);        free_vector(vv,1,n);  /* Doesn't work */
     tab=ivector(1,NCOVMAX);  ;
     ncodemax=ivector(1,NCOVMAX);  } 
   
     i=1;  void lubksb(double **a, int n, int *indx, double b[]) 
     while (fgets(line, MAXLINE, fic) != NULL)    {  { 
       if ((i >= firstobs) && (i <=lastobs)) {    int i,ii=0,ip,j; 
            double sum; 
         for (j=maxwav;j>=1;j--){   
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    for (i=1;i<=n;i++) { 
           strcpy(line,stra);      ip=indx[i]; 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      sum=b[ip]; 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      b[ip]=b[i]; 
         }      if (ii) 
                for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      else if (sum) ii=i; 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      b[i]=sum; 
     } 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    for (i=n;i>=1;i--) { 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      b[i]=sum/a[i][i]; 
         for (j=ncov;j>=1;j--){    } 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  } 
         }  
         num[i]=atol(stra);  /************ Frequencies ********************/
   void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
         /* printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/  {  /* Some frequencies */
     
         /*printf("%d %.lf %.lf %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),(covar[3][i]), (covar[4][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]));*/    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     int first;
         i=i+1;    double ***freq; /* Frequencies */
       }    double *pp, **prop;
     }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     /*scanf("%d",i);*/    FILE *ficresp;
     char fileresp[FILENAMELENGTH];
   imx=i-1; /* Number of individuals */    
      pp=vector(1,nlstate);
   /* Calculation of the number of parameter from char model*/    prop=matrix(1,nlstate,iagemin,iagemax+3);
   Tvar=ivector(1,8);        strcpy(fileresp,"p");
        strcat(fileresp,fileres);
   if (strlen(model) >1){    if((ficresp=fopen(fileresp,"w"))==NULL) {
     j=0;      printf("Problem with prevalence resultfile: %s\n", fileresp);
     j=nbocc(model,'+');      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     cptcovn=j+1;      exit(0);
      }
     strcpy(modelsav,model);    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     if (j==0) {    j1=0;
       cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb);    
     }    j=cptcoveff;
     else {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       for(i=j; i>=1;i--){  
         cutv(stra,strb,modelsav,'+');    first=1;
         if (strchr(strb,'*')) {  
           cutv(strd,strc,strb,'*');    for(k1=1; k1<=j;k1++){
           cutv(strb,stre,strc,'V');Tvar[i+1]=ncov+1;      for(i1=1; i1<=ncodemax[k1];i1++){
           cutv(strb,strc,strd,'V');        j1++;
           for (k=1; k<=lastobs;k++)        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
             covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          scanf("%d", i);*/
         }        for (i=-1; i<=nlstate+ndeath; i++)  
         else {          for (jk=-1; jk<=nlstate+ndeath; jk++)  
           cutv(strd,strc,strb,'V');            for(m=iagemin; m <= iagemax+3; m++)
           Tvar[i+1]=atoi(strc);              freq[i][jk][m]=0;
         }  
         strcpy(modelsav,stra);        for (i=1; i<=nlstate; i++)  
       }        for(m=iagemin; m <= iagemax+3; m++)
       /*cutv(strd,strc,stra,'V');*/          prop[i][m]=0;
       Tvar[1]=atoi(strc);        
     }        dateintsum=0;
   }        k2cpt=0;
   /*printf("tvar=%d ",Tvar[1]);*/        for (i=1; i<=imx; i++) {
   /*scanf("%d ",i);*/          bool=1;
     fclose(fic);          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
     if (weightopt != 1) { /* Maximisation without weights*/              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       for(i=1;i<=n;i++) weight[i]=1.0;                bool=0;
     }          }
     /*-calculation of age at interview from date of interview and age at death -*/          if (bool==1){
     agev=matrix(1,maxwav,1,imx);            for(m=firstpass; m<=lastpass; m++){
                  k2=anint[m][i]+(mint[m][i]/12.);
     for (i=1; i<=imx; i++)  {              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       for(m=1; (m<= maxwav); m++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         if (mint[m][i]==99 || anint[m][i]==9999) s[m][i]=-1;                  if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
         if(s[m][i] >0){                if (m<lastpass) {
           if (s[m][i] == nlstate+1) {                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
             if(agedc[i]>0)                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
               if(moisdc[i]!=99 && andc[i]!=9999)                }
               agev[m][i]=agedc[i];                
             else{                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                  dateintsum=dateintsum+k2;
               agev[m][i]=-1;                  k2cpt++;
             }                }
           }                /*}*/
           else if(s[m][i] !=9){ /* Should no more exist */            }
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          }
             if(mint[m][i]==99 || anint[m][i]==9999){        }
               agev[m][i]=1;         
               /* printf("i=%d m=%d agev=%lf \n",i,m, agev[m][i]);    */        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
             }  
             else if(agev[m][i] <agemin){        if  (cptcovn>0) {
               agemin=agev[m][i];          fprintf(ficresp, "\n#********** Variable "); 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             }          fprintf(ficresp, "**********\n#");
             else if(agev[m][i] >agemax){        }
               agemax=agev[m][i];        for(i=1; i<=nlstate;i++) 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
             }        fprintf(ficresp, "\n");
             /*agev[m][i]=anint[m][i]-annais[i];*/        
             /*   agev[m][i] = age[i]+2*m;*/        for(i=iagemin; i <= iagemax+3; i++){
           }          if(i==iagemax+3){
           else { /* =9 */            fprintf(ficlog,"Total");
             agev[m][i]=1;          }else{
             s[m][i]=-1;            if(first==1){
           }              first=0;
         }              printf("See log file for details...\n");
         else /*= 0 Unknown */            }
           agev[m][i]=1;            fprintf(ficlog,"Age %d", i);
       }          }
              for(jk=1; jk <=nlstate ; jk++){
     }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     for (i=1; i<=imx; i++)  {              pp[jk] += freq[jk][m][i]; 
       for(m=1; (m<= maxwav); m++){          }
         if (s[m][i] > (nlstate+ndeath)) {          for(jk=1; jk <=nlstate ; jk++){
           printf("Error: Wrong value in nlstate or ndeath\n");              for(m=-1, pos=0; m <=0 ; m++)
           goto end;              pos += freq[jk][m][i];
         }            if(pp[jk]>=1.e-10){
       }              if(first==1){
     }              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               }
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
     free_vector(severity,1,maxwav);              if(first==1)
     free_imatrix(outcome,1,maxwav+1,1,n);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     free_vector(moisnais,1,n);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     free_vector(annais,1,n);            }
     free_matrix(mint,1,maxwav,1,n);          }
     free_matrix(anint,1,maxwav,1,n);  
     free_vector(moisdc,1,n);          for(jk=1; jk <=nlstate ; jk++){
     free_vector(andc,1,n);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
              }       
     wav=ivector(1,imx);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            pos += pp[jk];
     mw=imatrix(1,lastpass-firstpass+1,1,imx);            posprop += prop[jk][i];
              }
     /* Concatenates waves */          for(jk=1; jk <=nlstate ; jk++){
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);            if(pos>=1.e-5){
               if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 Tcode=ivector(1,100);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
    nbcode=imatrix(1,nvar,1,8);              }else{
    ncodemax[1]=1;              if(first==1)
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
    codtab=imatrix(1,100,1,10);            }
    h=0;            if( i <= iagemax){
    m=pow(2,cptcovn);              if(pos>=1.e-5){
                  fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
    for(k=1;k<=cptcovn; k++){                /*probs[i][jk][j1]= pp[jk]/pos;*/
      for(i=1; i <=(m/pow(2,k));i++){                /*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(j=1; j <= ncodemax[k]; j++){              }
          for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){              else
            h++;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
            if (h>m) h=1;codtab[h][k]=j;            }
          }          }
        }          
      }          for(jk=-1; jk <=nlstate+ndeath; jk++)
    }            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
    /*for(i=1; i <=m ;i++){              if(first==1)
      for(k=1; k <=cptcovn; k++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
      }              }
      printf("\n");          if(i <= iagemax)
    }            fprintf(ficresp,"\n");
   scanf("%d",i);*/          if(first==1)
                printf("Others in log...\n");
    /* Calculates basic frequencies. Computes observed prevalence at single age          fprintf(ficlog,"\n");
        and prints on file fileres'p'. */        }
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);      }
     }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    dateintmean=dateintsum/k2cpt; 
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fclose(ficresp);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    free_vector(pp,1,nlstate);
        free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* For Powell, parameters are in a vector p[] starting at p[1]    /* End of Freq */
        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) */  
     /*scanf("%d",i);*/  /************ Prevalence ********************/
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  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)
   {  
        /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     /*--------- results files --------------*/       in each health status at the date of interview (if between dateprev1 and dateprev2).
     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);       We still use firstpass and lastpass as another selection.
        */
    jk=1;   
    fprintf(ficres,"# Parameters\n");    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
    printf("# Parameters\n");    double ***freq; /* Frequencies */
    for(i=1,jk=1; i <=nlstate; i++){    double *pp, **prop;
      for(k=1; k <=(nlstate+ndeath); k++){    double pos,posprop; 
        if (k != i)    double  y2; /* in fractional years */
          {    int iagemin, iagemax;
            printf("%d%d ",i,k);  
            fprintf(ficres,"%1d%1d ",i,k);    iagemin= (int) agemin;
            for(j=1; j <=ncovmodel; j++){    iagemax= (int) agemax;
              printf("%f ",p[jk]);    /*pp=vector(1,nlstate);*/
              fprintf(ficres,"%f ",p[jk]);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
              jk++;    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
            }    j1=0;
            printf("\n");    
            fprintf(ficres,"\n");    j=cptcoveff;
          }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      }    
    }    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
     /* Computing hessian and covariance matrix */        j1++;
     ftolhess=ftol; /* Usually correct */        
     hesscov(matcov, p, npar, delti, ftolhess, func);        for (i=1; i<=nlstate; i++)  
     fprintf(ficres,"# Scales\n");          for(m=iagemin; m <= iagemax+3; m++)
     printf("# Scales\n");            prop[i][m]=0.0;
      for(i=1,jk=1; i <=nlstate; i++){       
       for(j=1; j <=nlstate+ndeath; j++){        for (i=1; i<=imx; i++) { /* Each individual */
         if (j!=i) {          bool=1;
           fprintf(ficres,"%1d%1d",i,j);          if  (cptcovn>0) {
           printf("%1d%1d",i,j);            for (z1=1; z1<=cptcoveff; z1++) 
           for(k=1; k<=ncovmodel;k++){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
             printf(" %.5e",delti[jk]);                bool=0;
             fprintf(ficres," %.5e",delti[jk]);          } 
             jk++;          if (bool==1) { 
           }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
           printf("\n");              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
           fprintf(ficres,"\n");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                    if (s[m][i]>0 && s[m][i]<=nlstate) { 
     k=1;                  /*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(ficres,"# Covariance\n");                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     printf("# Covariance\n");                  prop[s[m][i]][iagemax+3] += weight[i]; 
     for(i=1;i<=npar;i++){                } 
       /*  if (k>nlstate) k=1;              }
       i1=(i-1)/(ncovmodel*nlstate)+1;            } /* end selection of waves */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          }
       printf("%s%d%d",alph[k],i1,tab[i]);*/        }
       fprintf(ficres,"%3d",i);        for(i=iagemin; i <= iagemax+3; i++){  
       printf("%3d",i);          
       for(j=1; j<=i;j++){          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         fprintf(ficres," %.5e",matcov[i][j]);            posprop += prop[jk][i]; 
         printf(" %.5e",matcov[i][j]);          } 
       }  
       fprintf(ficres,"\n");          for(jk=1; jk <=nlstate ; jk++){     
       printf("\n");            if( i <=  iagemax){ 
       k++;              if(posprop>=1.e-5){ 
     }                probs[i][jk][j1]= prop[jk][i]/posprop;
                  } 
     while((c=getc(ficpar))=='#' && c!= EOF){            } 
       ungetc(c,ficpar);          }/* end jk */ 
       fgets(line, MAXLINE, ficpar);        }/* end i */ 
       puts(line);      } /* end i1 */
       fputs(line,ficparo);    } /* end k1 */
     }    
     ungetc(c,ficpar);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
      /*free_vector(pp,1,nlstate);*/
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
      }  /* End of prevalence */
     if (fage <= 2) {  
       bage = agemin;  /************* Waves Concatenation ***************/
       fage = agemax;  
     }  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
   {
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);       Death is a valid wave (if date is known).
 /*------------ gnuplot -------------*/       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
 chdir(pathcd);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   if((ficgp=fopen("graph.plt","w"))==NULL) {       and mw[mi+1][i]. dh depends on stepm.
     printf("Problem with file graph.gp");goto end;       */
   }  
 #ifdef windows    int i, mi, m;
   fprintf(ficgp,"cd \"%s\" \n",pathc);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
 #endif       double sum=0., jmean=0.;*/
 m=pow(2,cptcovn);    int first;
      int j, k=0,jk, ju, jl;
  /* 1eme*/    double sum=0.;
   for (cpt=1; cpt<= nlstate ; cpt ++) {    first=0;
    for (k1=1; k1<= m ; k1 ++) {    jmin=1e+5;
     jmax=-1;
 #ifdef windows    jmean=0.;
     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);    for(i=1; i<=imx; i++){
 #endif      mi=0;
 #ifdef unix      m=firstpass;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      while(s[m][i] <= nlstate){
 #endif        if(s[m][i]>=1)
           mw[++mi][i]=m;
 for (i=1; i<= nlstate ; i ++) {        if(m >=lastpass)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          break;
   else fprintf(ficgp," \%%*lf (\%%*lf)");        else
 }          m++;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      }/* end while */
     for (i=1; i<= nlstate ; i ++) {      if (s[m][i] > nlstate){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        mi++;     /* Death is another wave */
   else fprintf(ficgp," \%%*lf (\%%*lf)");        /* if(mi==0)  never been interviewed correctly before death */
 }           /* Only death is a correct wave */
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        mw[mi][i]=m;
      for (i=1; i<= nlstate ; i ++) {      }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");      wav[i]=mi;
 }        if(mi==0){
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        nbwarn++;
 #ifdef unix        if(first==0){
 fprintf(ficgp,"\nset ter gif small size 400,300");          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
 #endif          first=1;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        }
    }        if(first==1){
   }          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
   /*2 eme*/        }
       } /* end mi==0 */
   for (k1=1; k1<= m ; k1 ++) {    } /* End individuals */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);  
        for(i=1; i<=imx; i++){
     for (i=1; i<= nlstate+1 ; i ++) {      for(mi=1; mi<wav[i];mi++){
       k=2*i;        if (stepm <=0)
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          dh[mi][i]=1;
       for (j=1; j<= nlstate+1 ; j ++) {        else{
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   else fprintf(ficgp," \%%*lf (\%%*lf)");            if (agedc[i] < 2*AGESUP) {
 }                j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");              if(j==0) j=1;  /* Survives at least one month after exam */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);              else if(j<0){
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);                nberr++;
       for (j=1; j<= nlstate+1 ; j ++) {                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                j=1; /* Temporary Dangerous patch */
         else fprintf(ficgp," \%%*lf (\%%*lf)");                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.\n  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(ficgp,"\" t\"\" w l 0,");                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.\n  You MUST fix the contradiction between dates.\n",stepm);
      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 ++) {              k=k+1;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              if (j >= jmax) jmax=j;
   else fprintf(ficgp," \%%*lf (\%%*lf)");              if (j <= jmin) jmin=j;
 }                sum=sum+j;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       else fprintf(ficgp,"\" t\"\" w l 0,");              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     }            }
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          }
   }          else{
              j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   /*3eme*/            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             k=k+1;
   for (k1=1; k1<= m ; k1 ++) {            if (j >= jmax) jmax=j;
     for (cpt=1; cpt<= nlstate ; cpt ++) {            else if (j <= jmin)jmin=j;
       k=2+nlstate*(cpt-1);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       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);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
       for (i=1; i< nlstate ; i ++) {            if(j<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);              nberr++;
       }              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              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]);
     }            }
   }            sum=sum+j;
            }
   /* CV preval stat */          jk= j/stepm;
   for (k1=1; k1<= m ; k1 ++) {          jl= j -jk*stepm;
     for (cpt=1; cpt<nlstate ; cpt ++) {          ju= j -(jk+1)*stepm;
       k=3;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);            if(jl==0){
       for (i=1; i< nlstate ; i ++)              dh[mi][i]=jk;
         fprintf(ficgp,"+$%d",k+i+1);              bh[mi][i]=0;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            }else{ /* We want a negative bias in order to only have interpolation ie
                          * at the price of an extra matrix product in likelihood */
       l=3+(nlstate+ndeath)*cpt;              dh[mi][i]=jk+1;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);              bh[mi][i]=ju;
       for (i=1; i< nlstate ; i ++) {            }
         l=3+(nlstate+ndeath)*cpt;          }else{
         fprintf(ficgp,"+$%d",l+i+1);            if(jl <= -ju){
       }              dh[mi][i]=jk;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                bh[mi][i]=jl;       /* bias is positive if real duration
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                                   * is higher than the multiple of stepm and negative otherwise.
     }                                   */
   }            }
             else{
   /* proba elementaires */              dh[mi][i]=jk+1;
   for(i=1,jk=1; i <=nlstate; i++){              bh[mi][i]=ju;
     for(k=1; k <=(nlstate+ndeath); k++){            }
       if (k != i) {            if(dh[mi][i]==0){
         /*  fprintf(ficgp,"%1d%1d ",i,k);*/              dh[mi][i]=1; /* At least one step */
         for(j=1; j <=ncovmodel; j++){              bh[mi][i]=ju; /* At least one step */
           fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);              /*  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);*/
           jk++;            }
           fprintf(ficgp,"\n");          } /* end if mle */
         }        }
       }      } /* end wave */
     }    }
   }    jmean=sum/k;
   for(jk=1; jk <=m; jk++) {    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   for(i=1; i <=nlstate; i++) {   }
     for(k=1; k <=(nlstate+ndeath); k++){  
       if (k != i) {  /*********** Tricode ****************************/
         fprintf(ficgp," exp(a%d%d+b%d%d*x",i,k,i,k);  void tricode(int *Tvar, int **nbcode, int imx)
         for(j=3; j <=ncovmodel; j++)  {
           fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    
         fprintf(ficgp,")/(1");    int Ndum[20],ij=1, k, j, i, maxncov=19;
         for(k1=1; k1 <=(nlstate+ndeath); k1++)    int cptcode=0;
           if (k1 != i) {    cptcoveff=0; 
             fprintf(ficgp,"+exp(a%d%d+b%d%d*x",i,k1,i,k1);   
             for(j=3; j <=ncovmodel; j++)    for (k=0; k<maxncov; k++) Ndum[k]=0;
               fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    for (k=1; k<=7; k++) ncodemax[k]=0;
             fprintf(ficgp,")");  
           }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
         fprintf(ficgp,") t \"p%d%d\" ", i,k);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
       if ((i+k)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                                 modality*/ 
       }        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     }        Ndum[ij]++; /*store the modality */
   }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
 fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);          if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   }                                         Tvar[j]. If V=sex and male is 0 and 
   fclose(ficgp);                                         female is 1, then  cptcode=1.*/
          }
 chdir(path);  
     free_matrix(agev,1,maxwav,1,imx);      for (i=0; i<=cptcode; i++) {
     free_ivector(wav,1,imx);        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 */
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      }
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);  
          ij=1; 
     free_imatrix(s,1,maxwav+1,1,n);      for (i=1; i<=ncodemax[j]; i++) {
            for (k=0; k<= maxncov; k++) {
              if (Ndum[k] != 0) {
     free_ivector(num,1,n);            nbcode[Tvar[j]][ij]=k; 
     free_vector(agedc,1,n);            /* 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; */
     free_vector(weight,1,n);            
     /*free_matrix(covar,1,NCOVMAX,1,n);*/            ij++;
     fclose(ficparo);          }
     fclose(ficres);          if (ij > ncodemax[j]) break; 
    }        }  
          } 
    /*________fin mle=1_________*/    }  
      
    for (k=0; k< maxncov; k++) Ndum[k]=0;
    
     /* No more information from the sample is required now */   for (i=1; i<=ncovmodel-2; i++) { 
   /* Reads comments: lines beginning with '#' */     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   while((c=getc(ficpar))=='#' && c!= EOF){     ij=Tvar[i];
     ungetc(c,ficpar);     Ndum[ij]++;
     fgets(line, MAXLINE, ficpar);   }
     puts(line);  
     fputs(line,ficparo);   ij=1;
   }   for (i=1; i<= maxncov; i++) {
   ungetc(c,ficpar);     if((Ndum[i]!=0) && (i<=ncovcol)){
         Tvaraff[ij]=i; /*For printing */
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);       ij++;
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);     }
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);   }
 /*--------- index.htm --------*/   
    cptcoveff=ij-1; /*Number of simple covariates*/
   if((fichtm=fopen("index.htm","w"))==NULL)    {  }
     printf("Problem with index.htm \n");goto end;  
   }  /*********** Health Expectancies ****************/
   
  fprintf(fichtm,"<body><ul> Imach, Version 0.63<hr> <li>Outputs files<br><br>\n  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
         - 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>  {
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    /* Health expectancies */
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    double age, agelim, hf;
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    double ***p3mat,***varhe;
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    double **dnewm,**doldm;
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    double *xp;
         - 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);    double **gp, **gm;
     double ***gradg, ***trgradg;
  fprintf(fichtm," <li>Graphs</li>\n<p>");    int theta;
   
  m=cptcovn;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    xp=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
  j1=0;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
  for(k1=1; k1<=m;k1++){    
    for(i1=1; i1<=ncodemax[k1];i1++){    fprintf(ficreseij,"# Health expectancies\n");
        j1++;    fprintf(ficreseij,"# Age");
        if (cptcovn > 0) {    for(i=1; i<=nlstate;i++)
          fprintf(fichtm,"<hr>************ Results for covariates");      for(j=1; j<=nlstate;j++)
          for (cpt=1; cpt<=cptcovn;cpt++)        fprintf(ficreseij," %1d-%1d (SE)",i,j);
            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);    fprintf(ficreseij,"\n");
          fprintf(fichtm," ************\n<hr>");  
        }    if(estepm < stepm){
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      printf ("Problem %d lower than %d\n",estepm, stepm);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        }
        for(cpt=1; cpt<nlstate;cpt++){    else  hstepm=estepm;   
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    /* We compute the life expectancy from trapezoids spaced every estepm months
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);     * This is mainly to measure the difference between two models: for example
        }     * if stepm=24 months pijx are given only every 2 years and by summing them
     for(cpt=1; cpt<=nlstate;cpt++) {     * we are calculating an estimate of the Life Expectancy assuming a linear 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident     * progression in between and thus overestimating or underestimating according
 interval) in state (%d): v%s%d%d.gif <br>     * to the curvature of the survival function. If, for the same date, we 
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);       * estimate the model with stepm=1 month, we can keep estepm to 24 months
      }     * to compare the new estimate of Life expectancy with the same linear 
      for(cpt=1; cpt<=nlstate;cpt++) {     * hypothesis. A more precise result, taking into account a more precise
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>     * curvature will be obtained if estepm is as small as stepm. */
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);  
      }    /* For example we decided to compute the life expectancy with the smallest unit */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 health expectancies in states (1) and (2): e%s%d.gif<br>       nhstepm is the number of hstepm from age to agelim 
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);       nstepm is the number of stepm from age to agelin. 
 fprintf(fichtm,"\n</body>");       Look at hpijx to understand the reason of that which relies in memory size
    }       and note for a fixed period like estepm months */
  }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 fclose(fichtm);       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
   /*--------------- Prevalence limit --------------*/       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.
   strcpy(filerespl,"pl");    */
   strcat(filerespl,fileres);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    agelim=AGESUP;
   }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      /* nhstepm age range expressed in number of stepm */
   fprintf(ficrespl,"#Prevalence limit\n");      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   fprintf(ficrespl,"#Age ");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      /* if (stepm >= YEARM) hstepm=1;*/
   fprintf(ficrespl,"\n");      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   prlim=matrix(1,nlstate,1,nlstate);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   k=0;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   agebase=agemin;   
   agelim=agemax;  
   ftolpl=1.e-10;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   i1=cptcovn;  
   if (cptcovn < 1){i1=1;}      /* Computing  Variances of health expectancies */
   
   for(cptcov=1;cptcov<=i1;cptcov++){       for(theta=1; theta <=npar; theta++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(i=1; i<=npar; i++){ 
         k=k+1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        }
         fprintf(ficrespl,"\n#****** ");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         for(j=1;j<=cptcovn;j++)    
           fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);        cptj=0;
         fprintf(ficrespl,"******\n");        for(j=1; j<= nlstate; j++){
                  for(i=1; i<=nlstate; i++){
         for (age=agebase; age<=agelim; age++){            cptj=cptj+1;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
           fprintf(ficrespl,"%.0f",age );              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           for(i=1; i<=nlstate;i++)            }
           fprintf(ficrespl," %.5f", prlim[i][i]);          }
           fprintf(ficrespl,"\n");        }
         }       
       }       
     }        for(i=1; i<=npar; i++) 
   fclose(ficrespl);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   /*------------- h Pij x at various ages ------------*/        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);        cptj=0;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        for(j=1; j<= nlstate; j++){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          for(i=1;i<=nlstate;i++){
   }            cptj=cptj+1;
   printf("Computing pij: result on file '%s' \n", filerespij);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
    
   stepsize=(int) (stepm+YEARM-1)/YEARM;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   if (stepm<=24) stepsize=2;            }
           }
   agelim=AGESUP;        }
   hstepm=stepsize*YEARM; /* Every year of age */        for(j=1; j<= nlstate*nlstate; j++)
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          for(h=0; h<=nhstepm-1; h++){
              gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   k=0;          }
   for(cptcov=1;cptcov<=i1;cptcov++){       } 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     
       k=k+1;  /* End theta */
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcovn;j++)       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);  
         fprintf(ficrespij,"******\n");       for(h=0; h<=nhstepm-1; h++)
                for(j=1; j<=nlstate*nlstate;j++)
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          for(theta=1; theta <=npar; theta++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            trgradg[h][j][theta]=gradg[h][theta][j];
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */       
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;       for(i=1;i<=nlstate*nlstate;i++)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for(j=1;j<=nlstate*nlstate;j++)
           fprintf(ficrespij,"# Age");          varhe[i][j][(int)age] =0.;
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)       printf("%d|",(int)age);fflush(stdout);
               fprintf(ficrespij," %1d-%1d",i,j);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           fprintf(ficrespij,"\n");       for(h=0;h<=nhstepm-1;h++){
           for (h=0; h<=nhstepm; h++){        for(k=0;k<=nhstepm-1;k++){
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
             for(i=1; i<=nlstate;i++)          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
               for(j=1; j<=nlstate+ndeath;j++)          for(i=1;i<=nlstate*nlstate;i++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            for(j=1;j<=nlstate*nlstate;j++)
             fprintf(ficrespij,"\n");              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
           }        }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
           fprintf(ficrespij,"\n");      /* Computing expectancies */
         }      for(i=1; i<=nlstate;i++)
     }        for(j=1; j<=nlstate;j++)
   }          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   fclose(ficrespij);            
   /* 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]);*/
   /*---------- Health expectancies and variances ------------*/  
           }
   strcpy(filerest,"t");  
   strcat(filerest,fileres);      fprintf(ficreseij,"%3.0f",age );
   if((ficrest=fopen(filerest,"w"))==NULL) {      cptj=0;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      for(i=1; i<=nlstate;i++)
   }        for(j=1; j<=nlstate;j++){
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          cptj++;
           fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
         }
   strcpy(filerese,"e");      fprintf(ficreseij,"\n");
   strcat(filerese,fileres);     
   if((ficreseij=fopen(filerese,"w"))==NULL) {      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  strcpy(fileresv,"v");    }
   strcat(fileresv,fileres);    printf("\n");
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    fprintf(ficlog,"\n");
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }    free_vector(xp,1,npar);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   k=0;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   for(cptcov=1;cptcov<=i1;cptcov++){  }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;  /************ Variance ******************/
       fprintf(ficrest,"\n#****** ");  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
       for(j=1;j<=cptcovn;j++)  {
         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);    /* Variance of health expectancies */
       fprintf(ficrest,"******\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
       fprintf(ficreseij,"\n#****** ");    double **dnewm,**doldm;
       for(j=1;j<=cptcovn;j++)    double **dnewmp,**doldmp;
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    int i, j, nhstepm, hstepm, h, nstepm ;
       fprintf(ficreseij,"******\n");    int k, cptcode;
     double *xp;
       fprintf(ficresvij,"\n#****** ");    double **gp, **gm;  /* for var eij */
       for(j=1;j<=cptcovn;j++)    double ***gradg, ***trgradg; /*for var eij */
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    double **gradgp, **trgradgp; /* for var p point j */
       fprintf(ficresvij,"******\n");    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double ***p3mat;
       oldm=oldms;savm=savms;    double age,agelim, hf;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      double ***mobaverage;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    int theta;
       oldm=oldms;savm=savms;    char digit[4];
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    char digitp[25];
        
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    char fileresprobmorprev[FILENAMELENGTH];
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  
       fprintf(ficrest,"\n");    if(popbased==1){
              if(mobilav!=0)
       hf=1;        strcpy(digitp,"-populbased-mobilav-");
       if (stepm >= YEARM) hf=stepm/YEARM;      else strcpy(digitp,"-populbased-nomobil-");
       epj=vector(1,nlstate+1);    }
       for(age=bage; age <=fage ;age++){    else 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      strcpy(digitp,"-stablbased-");
         fprintf(ficrest," %.0f",age);  
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    if (mobilav!=0) {
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           epj[nlstate+1] +=epj[j];        printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }      }
         for(i=1, vepp=0.;i <=nlstate;i++)    }
           for(j=1;j <=nlstate;j++)  
             vepp += vareij[i][j][(int)age];    strcpy(fileresprobmorprev,"prmorprev"); 
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    sprintf(digit,"%-d",ij);
         for(j=1;j <=nlstate;j++){    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    strcat(fileresprobmorprev,digit); /* Tvar to be done */
         }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         fprintf(ficrest,"\n");    strcat(fileresprobmorprev,fileres);
       }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
            }
  fclose(ficreseij);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
  fclose(ficresvij);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   fclose(ficrest);    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);
   fclose(ficpar);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   free_vector(epj,1,nlstate+1);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   /*  scanf("%d ",i); */      fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
   /*------- Variance limit prevalence------*/          fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
 strcpy(fileresvpl,"vpl");    fprintf(ficresprobmorprev,"\n");
   strcat(fileresvpl,fileres);    fprintf(ficgp,"\n# Routine varevsij");
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    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");
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     exit(0);  /*   } */
   }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
     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");
  k=0;    fprintf(ficresvij,"# Age");
  for(cptcov=1;cptcov<=i1;cptcov++){    for(i=1; i<=nlstate;i++)
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(j=1; j<=nlstate;j++)
      k=k+1;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
      fprintf(ficresvpl,"\n#****** ");    fprintf(ficresvij,"\n");
      for(j=1;j<=cptcovn;j++)  
        fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);    xp=vector(1,npar);
      fprintf(ficresvpl,"******\n");    dnewm=matrix(1,nlstate,1,npar);
          doldm=matrix(1,nlstate,1,nlstate);
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
      oldm=oldms;savm=savms;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
    }    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
  }    gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
   fclose(ficresvpl);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
   /*---------- End : free ----------------*/    if(estepm < stepm){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      printf ("Problem %d lower than %d\n",estepm, stepm);
      }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    else  hstepm=estepm;   
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    /* 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 
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);       nstepm is the number of stepm from age to agelin. 
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);       Look at hpijx to understand the reason of that which relies in memory size
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);       and note for a fixed period like k years */
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    /* 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
   free_matrix(matcov,1,npar,1,npar);       means that if the survival funtion is printed every two years of age and if
   free_vector(delti,1,npar);       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.
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   printf("End of Imach\n");    agelim = AGESUP;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   /* 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);*/      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   /*printf("Total time was %d uSec.\n", total_usecs);*/      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*------ End -----------*/      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
  end:      gm=matrix(0,nhstepm,1,nlstate);
 #ifdef windows  
  chdir(pathcd);  
 #endif      for(theta=1; theta <=npar; theta++){
  system("wgnuplot ../gp37mgw/graph.plt");        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
 #ifdef windows        }
   while (z[0] != 'q') {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     chdir(pathcd);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");  
     scanf("%s",z);        if (popbased==1) {
     if (z[0] == 'c') system("./imach");          if(mobilav ==0){
     else if (z[0] == 'e') {            for(i=1; i<=nlstate;i++)
       chdir(path);              prlim[i][i]=probs[(int)age][i][ij];
       system("index.htm");          }else{ /* mobilav */ 
     }            for(i=1; i<=nlstate;i++)
     else if (z[0] == 'q') exit(0);              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
 #endif        }
 }    
         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)
   {
     /* 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,"# 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)
   {
     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,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     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><h4>Result files (first order: no variance)</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> Result files (second order: variances)</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 */
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     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]; 
     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;
     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;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     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(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%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: ");
     fprintf(ficlog,"pathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",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 */
    
     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);
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     /* 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);
   
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     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);
   
     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++){
       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 paramater 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);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter 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){
           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); 
   
     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);
     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 */
     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);
   
     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*/
     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.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     /*  fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);*/
   
     /*  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,"#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,"#****** 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);
   
     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);  
    
         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);
         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);
         }
   
    
         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);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     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);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     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\nLocaltime 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);
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     if((outcmd=system(plotcmd)) != 0){
       printf(" 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') 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.1.2  
changed lines
  Added in v.1.97

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