Diff for /imach/src/imach.c between versions 1.18 and 1.103

version 1.18, 2002/02/20 17:17:09 version 1.103, 2005/09/30 15:54:49
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.103  2005/09/30 15:54:49  lievre
   individuals from different ages are interviewed on their health status    (Module): sump fixed, loop imx fixed, and simplifications.
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.102  2004/09/15 17:31:30  brouard
   Health expectancies are computed from the transistions observed between    Add the possibility to read data file including tab characters.
   waves and are computed for each degree of severity of disability (number  
   of life states). More degrees you consider, more time is necessary to    Revision 1.101  2004/09/15 10:38:38  brouard
   reach the Maximum Likelihood of the parameters involved in the model.    Fix on curr_time
   The simplest model is the multinomial logistic model where pij is  
   the probabibility to be observed in state j at the second wave conditional    Revision 1.100  2004/07/12 18:29:06  brouard
   to be observed in state i at the first wave. Therefore the model is:    Add version for Mac OS X. Just define UNIX in Makefile
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'  
   is a covariate. If you want to have a more complex model than "constant and    Revision 1.99  2004/06/05 08:57:40  brouard
   age", you should modify the program where the markup    *** empty log message ***
     *Covariates have to be included here again* invites you to do it.  
   More covariates you add, less is the speed of the convergence.    Revision 1.98  2004/05/16 15:05:56  brouard
     New version 0.97 . First attempt to estimate force of mortality
   The advantage that this computer programme claims, comes from that if the    directly from the data i.e. without the need of knowing the health
   delay between waves is not identical for each individual, or if some    state at each age, but using a Gompertz model: log u =a + b*age .
   individual missed an interview, the information is not rounded or lost, but    This is the basic analysis of mortality and should be done before any
   taken into account using an interpolation or extrapolation.    other analysis, in order to test if the mortality estimated from the
   hPijx is the probability to be    cross-longitudinal survey is different from the mortality estimated
   observed in state i at age x+h conditional to the observed state i at age    from other sources like vital statistic data.
   x. The delay 'h' can be split into an exact number (nh*stepm) of  
   unobserved intermediate  states. This elementary transition (by month or    The same imach parameter file can be used but the option for mle should be -3.
   quarter trimester, semester or year) is model as a multinomial logistic.  
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    Agnès, who wrote this part of the code, tried to keep most of the
   and the contribution of each individual to the likelihood is simply hPijx.    former routines in order to include the new code within the former code.
   
   Also this programme outputs the covariance matrix of the parameters but also    The output is very simple: only an estimate of the intercept and of
   of the life expectancies. It also computes the prevalence limits.    the slope with 95% confident intervals.
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Current limitations:
            Institut national d'études démographiques, Paris.    A) Even if you enter covariates, i.e. with the
   This software have been partly granted by Euro-REVES, a concerted action    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   from the European Union.    B) There is no computation of Life Expectancy nor Life Table.
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.97  2004/02/20 13:25:42  lievre
   can be accessed at http://euroreves.ined.fr/imach .    Version 0.96d. Population forecasting command line is (temporarily)
   **********************************************************************/    suppressed.
    
 #include <math.h>    Revision 1.96  2003/07/15 15:38:55  brouard
 #include <stdio.h>    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #include <stdlib.h>    rewritten within the same printf. Workaround: many printfs.
 #include <unistd.h>  
     Revision 1.95  2003/07/08 07:54:34  brouard
 #define MAXLINE 256    * imach.c (Repository):
 #define FILENAMELENGTH 80    (Repository): Using imachwizard code to output a more meaningful covariance
 /*#define DEBUG*/    matrix (cov(a12,c31) instead of numbers.
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.94  2003/06/27 13:00:02  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Just cleaning
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.93  2003/06/25 16:33:55  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 #define NINTERVMAX 8    (Module): Version 0.96b
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.92  2003/06/25 16:30:45  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    (Module): On windows (cygwin) function asctime_r doesn't
 #define MAXN 20000    exist so I changed back to asctime which exists.
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.91  2003/06/25 15:30:29  brouard
 #define AGEBASE 40    * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
 int nvar;    is stamped in powell.  We created a new html file for the graphs
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    concerning matrix of covariance. It has extension -cov.htm.
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Revision 1.90  2003/06/24 12:34:15  brouard
 int ndeath=1; /* Number of dead states */    (Module): Some bugs corrected for windows. Also, when
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    mle=-1 a template is output in file "or"mypar.txt with the design
 int popbased=0;    of the covariance matrix to be input.
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.89  2003/06/24 12:30:52  brouard
 int maxwav; /* Maxim number of waves */    (Module): Some bugs corrected for windows. Also, when
 int jmin, jmax; /* min, max spacing between 2 waves */    mle=-1 a template is output in file "or"mypar.txt with the design
 int mle, weightopt;    of the covariance matrix to be input.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.88  2003/06/23 17:54:56  brouard
 double jmean; /* Mean space between 2 waves */    * 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.
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.87  2003/06/18 12:26:01  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    Version 0.96
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;  
 FILE *ficreseij;    Revision 1.86  2003/06/17 20:04:08  brouard
   char filerese[FILENAMELENGTH];    (Module): Change position of html and gnuplot routines and added
  FILE  *ficresvij;    routine fileappend.
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.85  2003/06/17 13:12:43  brouard
   char fileresvpl[FILENAMELENGTH];    * imach.c (Repository): Check when date of death was earlier that
     current date of interview. It may happen when the death was just
 #define NR_END 1    prior to the death. In this case, dh was negative and likelihood
 #define FREE_ARG char*    was wrong (infinity). We still send an "Error" but patch by
 #define FTOL 1.0e-10    assuming that the date of death was just one stepm after the
     interview.
 #define NRANSI    (Repository): Because some people have very long ID (first column)
 #define ITMAX 200    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
 #define TOL 2.0e-4    truncation)
     (Repository): No more line truncation errors.
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.84  2003/06/13 21:44:43  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    * imach.c (Repository): Replace "freqsummary" at a correct
     place. It differs from routine "prevalence" which may be called
 #define GOLD 1.618034    many times. Probs is memory consuming and must be used with
 #define GLIMIT 100.0    parcimony.
 #define TINY 1.0e-20    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
 static double maxarg1,maxarg2;    Revision 1.83  2003/06/10 13:39:11  lievre
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    *** empty log message ***
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.82  2003/06/05 15:57:20  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Add log in  imach.c and  fullversion number is now printed.
 #define rint(a) floor(a+0.5)  
   */
 static double sqrarg;  /*
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)     Interpolated Markov Chain
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Short summary of the programme:
 int imx;    
 int stepm;    This program computes Healthy Life Expectancies from
 /* Stepm, step in month: minimum step interpolation*/    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
 int m,nb;    interviewed on their health status or degree of disability (in the
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    case of a health survey which is our main interest) -2- at least a
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    second wave of interviews ("longitudinal") which measure each change
 double **pmmij, ***probs, ***mobaverage;    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
 double *weight;    model. More health states you consider, more time is necessary to reach the
 int **s; /* Status */    Maximum Likelihood of the parameters involved in the model.  The
 double *agedc, **covar, idx;    simplest model is the multinomial logistic model where pij is the
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    probability to be observed in state j at the second wave
     conditional to be observed in state i at the first wave. Therefore
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 double ftolhess; /* Tolerance for computing hessian */    '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
 /**************** split *************************/    where the markup *Covariates have to be included here again* invites
 static  int split( char *path, char *dirc, char *name )    you to do it.  More covariates you add, slower the
 {    convergence.
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
    l1 = strlen( path );                 /* length of path */    identical for each individual. Also, if a individual missed an
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    intermediate interview, the information is lost, but taken into
    s = strrchr( path, '\\' );           /* find last / */    account using an interpolation or extrapolation.  
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    hPijx is the probability to be observed in state i at age x+h
       extern char       *getwd( );    conditional to the observed state i at age x. The delay 'h' can be
     split into an exact number (nh*stepm) of unobserved intermediate
       if ( getwd( dirc ) == NULL ) {    states. This elementary transition (by month, quarter,
 #else    semester or year) is modelled as a multinomial logistic.  The hPx
       extern char       *getcwd( );    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    hPijx.
 #endif  
          return( GLOCK_ERROR_GETCWD );    Also this programme outputs the covariance matrix of the parameters but also
       }    of the life expectancies. It also computes the stable prevalence. 
       strcpy( name, path );             /* we've got it */    
    } else {                             /* strip direcotry from path */    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
       s++;                              /* after this, the filename */             Institut national d'études démographiques, Paris.
       l2 = strlen( s );                 /* length of filename */    This software have been partly granted by Euro-REVES, a concerted action
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    from the European Union.
       strcpy( name, s );                /* save file name */    It is copyrighted identically to a GNU software product, ie programme and
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    software can be distributed freely for non commercial use. Latest version
       dirc[l1-l2] = 0;                  /* add zero */    can be accessed at http://euroreves.ined.fr/imach .
    }  
    l1 = strlen( dirc );                 /* length of directory */    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
    return( 0 );                         /* we're done */    
 }    **********************************************************************/
   /*
     main
 /******************************************/    read parameterfile
     read datafile
 void replace(char *s, char*t)    concatwav
 {    freqsummary
   int i;    if (mle >= 1)
   int lg=20;      mlikeli
   i=0;    print results files
   lg=strlen(t);    if mle==1 
   for(i=0; i<= lg; i++) {       computes hessian
     (s[i] = t[i]);    read end of parameter file: agemin, agemax, bage, fage, estepm
     if (t[i]== '\\') s[i]='/';        begin-prev-date,...
   }    open gnuplot file
 }    open html file
     stable prevalence
 int nbocc(char *s, char occ)     for age prevalim()
 {    h Pij x
   int i,j=0;    variance of p varprob
   int lg=20;    forecasting if prevfcast==1 prevforecast call prevalence()
   i=0;    health expectancies
   lg=strlen(s);    Variance-covariance of DFLE
   for(i=0; i<= lg; i++) {    prevalence()
   if  (s[i] == occ ) j++;     movingaverage()
   }    varevsij() 
   return j;    if popbased==1 varevsij(,popbased)
 }    total life expectancies
     Variance of stable prevalence
 void cutv(char *u,char *v, char*t, char occ)   end
 {  */
   int i,lg,j,p=0;  
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;   
   }  #include <math.h>
   #include <stdio.h>
   lg=strlen(t);  #include <stdlib.h>
   for(j=0; j<p; j++) {  #include <unistd.h>
     (u[j] = t[j]);  
   }  /* #include <sys/time.h> */
      u[p]='\0';  #include <time.h>
   #include "timeval.h"
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);  /* #include <libintl.h> */
   }  /* #define _(String) gettext (String) */
 }  
   #define MAXLINE 256
 /********************** nrerror ********************/  #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 void nrerror(char error_text[])  #define FILENAMELENGTH 132
 {  /*#define DEBUG*/
   fprintf(stderr,"ERREUR ...\n");  /*#define windows*/
   fprintf(stderr,"%s\n",error_text);  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   exit(1);  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 }  
 /*********************** vector *******************/  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 double *vector(int nl, int nh)  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 {  
   double *v;  #define NINTERVMAX 8
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   if (!v) nrerror("allocation failure in vector");  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   return v-nl+NR_END;  #define NCOVMAX 8 /* Maximum number of covariates */
 }  #define MAXN 20000
   #define YEARM 12. /* Number of months per year */
 /************************ free vector ******************/  #define AGESUP 130
 void free_vector(double*v, int nl, int nh)  #define AGEBASE 40
 {  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   free((FREE_ARG)(v+nl-NR_END));  #ifdef UNIX
 }  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 /************************ivector *******************************/  #else
 int *ivector(long nl,long nh)  #define DIRSEPARATOR '\\'
 {  #define ODIRSEPARATOR '/'
   int *v;  #endif
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  /* $Id$ */
   return v-nl+NR_END;  /* $State$ */
 }  
   char version[]="Imach version 0.97c, September 2004, INED-EUROREVES ";
 /******************free ivector **************************/  char fullversion[]="$Revision$ $Date$"; 
 void free_ivector(int *v, long nl, long nh)  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 {  int nvar;
   free((FREE_ARG)(v+nl-NR_END));  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 }  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
 /******************* imatrix *******************************/  int ndeath=1; /* Number of dead states */
 int **imatrix(long nrl, long nrh, long ncl, long nch)  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  int popbased=0;
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  int *wav; /* Number of waves for this individuual 0 is possible */
   int **m;  int maxwav; /* Maxim number of waves */
    int jmin, jmax; /* min, max spacing between 2 waves */
   /* allocate pointers to rows */  int gipmx, gsw; /* Global variables on the number of contributions 
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));                     to the likelihood and the sum of weights (done by funcone)*/
   if (!m) nrerror("allocation failure 1 in matrix()");  int mle, weightopt;
   m += NR_END;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   m -= nrl;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
    int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
               * wave mi and wave mi+1 is not an exact multiple of stepm. */
   /* allocate rows and set pointers to them */  double jmean; /* Mean space between 2 waves */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  double **oldm, **newm, **savm; /* Working pointers to matrices */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   m[nrl] += NR_END;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   m[nrl] -= ncl;  FILE *ficlog, *ficrespow;
    int globpr; /* Global variable for printing or not */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  double fretone; /* Only one call to likelihood */
    long ipmx; /* Number of contributions */
   /* return pointer to array of pointers to rows */  double sw; /* Sum of weights */
   return m;  char filerespow[FILENAMELENGTH];
 }  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   FILE *ficresilk;
 /****************** free_imatrix *************************/  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 void free_imatrix(m,nrl,nrh,ncl,nch)  FILE *ficresprobmorprev;
       int **m;  FILE *fichtm, *fichtmcov; /* Html File */
       long nch,ncl,nrh,nrl;  FILE *ficreseij;
      /* free an int matrix allocated by imatrix() */  char filerese[FILENAMELENGTH];
 {  FILE  *ficresvij;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  char fileresv[FILENAMELENGTH];
   free((FREE_ARG) (m+nrl-NR_END));  FILE  *ficresvpl;
 }  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
 /******************* matrix *******************************/  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 double **matrix(long nrl, long nrh, long ncl, long nch)  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 {  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  char command[FILENAMELENGTH];
   double **m;  int  outcmd=0;
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  char filelog[FILENAMELENGTH]; /* Log file */
   m -= nrl;  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  char popfile[FILENAMELENGTH];
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   m[nrl] -= ncl;  
   struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  struct timezone tzp;
   return m;  extern int gettimeofday();
 }  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   long time_value;
 /*************************free matrix ************************/  extern long time();
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  char strcurr[80], strfor[80];
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define NR_END 1
   free((FREE_ARG)(m+nrl-NR_END));  #define FREE_ARG char*
 }  #define FTOL 1.0e-10
   
 /******************* ma3x *******************************/  #define NRANSI 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  #define ITMAX 200 
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  #define TOL 2.0e-4 
   double ***m;  
   #define CGOLD 0.3819660 
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define ZEPS 1.0e-10 
   if (!m) nrerror("allocation failure 1 in matrix()");  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   m += NR_END;  
   m -= nrl;  #define GOLD 1.618034 
   #define GLIMIT 100.0 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define TINY 1.0e-20 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  static double maxarg1,maxarg2;
   m[nrl] -= ncl;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #define rint(a) floor(a+0.5)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  static double sqrarg;
   m[nrl][ncl] -= nll;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   for (j=ncl+1; j<=nch; j++)  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
     m[nrl][j]=m[nrl][j-1]+nlay;  int agegomp= AGEGOMP;
    
   for (i=nrl+1; i<=nrh; i++) {  int imx; 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  int stepm=1;
     for (j=ncl+1; j<=nch; j++)  /* Stepm, step in month: minimum step interpolation*/
       m[i][j]=m[i][j-1]+nlay;  
   }  int estepm;
   return m;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 }  
   int m,nb;
 /*************************free ma3x ************************/  long *num;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  double **pmmij, ***probs;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  double *ageexmed,*agecens;
   free((FREE_ARG)(m+nrl-NR_END));  double dateintmean=0;
 }  
   double *weight;
 /***************** f1dim *************************/  int **s; /* Status */
 extern int ncom;  double *agedc, **covar, idx;
 extern double *pcom,*xicom;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 extern double (*nrfunc)(double []);  
    double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 double f1dim(double x)  double ftolhess; /* Tolerance for computing hessian */
 {  
   int j;  /**************** split *************************/
   double f;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   double *xt;  {
      /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
   xt=vector(1,ncom);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    */ 
   f=(*nrfunc)(xt);    char  *ss;                            /* pointer */
   free_vector(xt,1,ncom);    int   l1, l2;                         /* length counters */
   return f;  
 }    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 /*****************brent *************************/    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    if ( ss == NULL ) {                   /* no directory, so use current */
 {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   int iter;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   double a,b,d,etemp;      /* get current working directory */
   double fu,fv,fw,fx;      /*    extern  char* getcwd ( char *buf , int len);*/
   double ftemp;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   double p,q,r,tol1,tol2,u,v,w,x,xm;        return( GLOCK_ERROR_GETCWD );
   double e=0.0;      }
        strcpy( name, path );               /* we've got it */
   a=(ax < cx ? ax : cx);    } else {                              /* strip direcotry from path */
   b=(ax > cx ? ax : cx);      ss++;                               /* after this, the filename */
   x=w=v=bx;      l2 = strlen( ss );                  /* length of filename */
   fw=fv=fx=(*f)(x);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   for (iter=1;iter<=ITMAX;iter++) {      strcpy( name, ss );         /* save file name */
     xm=0.5*(a+b);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);      dirc[l1-l2] = 0;                    /* add zero */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    }
     printf(".");fflush(stdout);    l1 = strlen( dirc );                  /* length of directory */
 #ifdef DEBUG    /*#ifdef windows
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  #else
 #endif    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  #endif
       *xmin=x;    */
       return fx;    ss = strrchr( name, '.' );            /* find last / */
     }    if (ss >0){
     ftemp=fu;      ss++;
     if (fabs(e) > tol1) {      strcpy(ext,ss);                     /* save extension */
       r=(x-w)*(fx-fv);      l1= strlen( name);
       q=(x-v)*(fx-fw);      l2= strlen(ss)+1;
       p=(x-v)*q-(x-w)*r;      strncpy( finame, name, l1-l2);
       q=2.0*(q-r);      finame[l1-l2]= 0;
       if (q > 0.0) p = -p;    }
       q=fabs(q);    return( 0 );                          /* we're done */
       etemp=e;  }
       e=d;  
       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;  void replace_back_to_slash(char *s, char*t)
         u=x+d;  {
         if (u-a < tol2 || b-u < tol2)    int i;
           d=SIGN(tol1,xm-x);    int lg=0;
       }    i=0;
     } else {    lg=strlen(t);
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    for(i=0; i<= lg; i++) {
     }      (s[i] = t[i]);
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));      if (t[i]== '\\') s[i]='/';
     fu=(*f)(u);    }
     if (fu <= fx) {  }
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  int nbocc(char *s, char occ)
         SHFT(fv,fw,fx,fu)  {
         } else {    int i,j=0;
           if (u < x) a=u; else b=u;    int lg=20;
           if (fu <= fw || w == x) {    i=0;
             v=w;    lg=strlen(s);
             w=u;    for(i=0; i<= lg; i++) {
             fv=fw;    if  (s[i] == occ ) j++;
             fw=fu;    }
           } else if (fu <= fv || v == x || v == w) {    return j;
             v=u;  }
             fv=fu;  
           }  void cutv(char *u,char *v, char*t, char occ)
         }  {
   }    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
   nrerror("Too many iterations in brent");       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
   *xmin=x;       gives u="abcedf" and v="ghi2j" */
   return fx;    int i,lg,j,p=0;
 }    i=0;
     for(j=0; j<=strlen(t)-1; j++) {
 /****************** mnbrak ***********************/      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     }
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))    lg=strlen(t);
 {    for(j=0; j<p; j++) {
   double ulim,u,r,q, dum;      (u[j] = t[j]);
   double fu;    }
         u[p]='\0';
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);     for(j=0; j<= lg; j++) {
   if (*fb > *fa) {      if (j>=(p+1))(v[j-p-1] = t[j]);
     SHFT(dum,*ax,*bx,dum)    }
       SHFT(dum,*fb,*fa,dum)  }
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);  /********************** nrerror ********************/
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  void nrerror(char error_text[])
     r=(*bx-*ax)*(*fb-*fc);  {
     q=(*bx-*cx)*(*fb-*fa);    fprintf(stderr,"ERREUR ...\n");
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    fprintf(stderr,"%s\n",error_text);
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    exit(EXIT_FAILURE);
     ulim=(*bx)+GLIMIT*(*cx-*bx);  }
     if ((*bx-u)*(u-*cx) > 0.0) {  /*********************** vector *******************/
       fu=(*func)(u);  double *vector(int nl, int nh)
     } else if ((*cx-u)*(u-ulim) > 0.0) {  {
       fu=(*func)(u);    double *v;
       if (fu < *fc) {    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    if (!v) nrerror("allocation failure in vector");
           SHFT(*fb,*fc,fu,(*func)(u))    return v-nl+NR_END;
           }  }
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  /************************ free vector ******************/
       fu=(*func)(u);  void free_vector(double*v, int nl, int nh)
     } else {  {
       u=(*cx)+GOLD*(*cx-*bx);    free((FREE_ARG)(v+nl-NR_END));
       fu=(*func)(u);  }
     }  
     SHFT(*ax,*bx,*cx,u)  /************************ivector *******************************/
       SHFT(*fa,*fb,*fc,fu)  int *ivector(long nl,long nh)
       }  {
 }    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 /*************** linmin ************************/    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
 int ncom;  }
 double *pcom,*xicom;  
 double (*nrfunc)(double []);  /******************free ivector **************************/
    void free_ivector(int *v, long nl, long nh)
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  {
 {    free((FREE_ARG)(v+nl-NR_END));
   double brent(double ax, double bx, double cx,  }
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);  /************************lvector *******************************/
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  long *lvector(long nl,long nh)
               double *fc, double (*func)(double));  {
   int j;    long *v;
   double xx,xmin,bx,ax;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   double fx,fb,fa;    if (!v) nrerror("allocation failure in ivector");
      return v-nl+NR_END;
   ncom=n;  }
   pcom=vector(1,n);  
   xicom=vector(1,n);  /******************free lvector **************************/
   nrfunc=func;  void free_lvector(long *v, long nl, long nh)
   for (j=1;j<=n;j++) {  {
     pcom[j]=p[j];    free((FREE_ARG)(v+nl-NR_END));
     xicom[j]=xi[j];  }
   }  
   ax=0.0;  /******************* imatrix *******************************/
   xx=1.0;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  { 
 #ifdef DEBUG    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    int **m; 
 #endif    
   for (j=1;j<=n;j++) {    /* allocate pointers to rows */ 
     xi[j] *= xmin;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     p[j] += xi[j];    if (!m) nrerror("allocation failure 1 in matrix()"); 
   }    m += NR_END; 
   free_vector(xicom,1,n);    m -= nrl; 
   free_vector(pcom,1,n);    
 }    
     /* allocate rows and set pointers to them */ 
 /*************** powell ************************/    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
             double (*func)(double []))    m[nrl] += NR_END; 
 {    m[nrl] -= ncl; 
   void linmin(double p[], double xi[], int n, double *fret,    
               double (*func)(double []));    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   int i,ibig,j;    
   double del,t,*pt,*ptt,*xit;    /* return pointer to array of pointers to rows */ 
   double fp,fptt;    return m; 
   double *xits;  } 
   pt=vector(1,n);  
   ptt=vector(1,n);  /****************** free_imatrix *************************/
   xit=vector(1,n);  void free_imatrix(m,nrl,nrh,ncl,nch)
   xits=vector(1,n);        int **m;
   *fret=(*func)(p);        long nch,ncl,nrh,nrl; 
   for (j=1;j<=n;j++) pt[j]=p[j];       /* free an int matrix allocated by imatrix() */ 
   for (*iter=1;;++(*iter)) {  { 
     fp=(*fret);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     ibig=0;    free((FREE_ARG) (m+nrl-NR_END)); 
     del=0.0;  } 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     for (i=1;i<=n;i++)  /******************* matrix *******************************/
       printf(" %d %.12f",i, p[i]);  double **matrix(long nrl, long nrh, long ncl, long nch)
     printf("\n");  {
     for (i=1;i<=n;i++) {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    double **m;
       fptt=(*fret);  
 #ifdef DEBUG    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       printf("fret=%lf \n",*fret);    if (!m) nrerror("allocation failure 1 in matrix()");
 #endif    m += NR_END;
       printf("%d",i);fflush(stdout);    m -= nrl;
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         del=fabs(fptt-(*fret));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         ibig=i;    m[nrl] += NR_END;
       }    m[nrl] -= ncl;
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       for (j=1;j<=n;j++) {    return m;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
         printf(" x(%d)=%.12e",j,xit[j]);     */
       }  }
       for(j=1;j<=n;j++)  
         printf(" p=%.12e",p[j]);  /*************************free matrix ************************/
       printf("\n");  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
 #endif  {
     }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    free((FREE_ARG)(m+nrl-NR_END));
 #ifdef DEBUG  }
       int k[2],l;  
       k[0]=1;  /******************* ma3x *******************************/
       k[1]=-1;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       printf("Max: %.12e",(*func)(p));  {
       for (j=1;j<=n;j++)    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
         printf(" %.12e",p[j]);    double ***m;
       printf("\n");  
       for(l=0;l<=1;l++) {    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         for (j=1;j<=n;j++) {    if (!m) nrerror("allocation failure 1 in matrix()");
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    m += 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;
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 #endif    m[nrl] += NR_END;
     m[nrl] -= ncl;
   
       free_vector(xit,1,n);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       free_vector(pt,1,n);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       return;    m[nrl][ncl] += NR_END;
     }    m[nrl][ncl] -= nll;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    for (j=ncl+1; j<=nch; j++) 
     for (j=1;j<=n;j++) {      m[nrl][j]=m[nrl][j-1]+nlay;
       ptt[j]=2.0*p[j]-pt[j];    
       xit[j]=p[j]-pt[j];    for (i=nrl+1; i<=nrh; i++) {
       pt[j]=p[j];      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     }      for (j=ncl+1; j<=nch; j++) 
     fptt=(*func)(ptt);        m[i][j]=m[i][j-1]+nlay;
     if (fptt < fp) {    }
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    return m; 
       if (t < 0.0) {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         linmin(p,xit,n,fret,func);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
         for (j=1;j<=n;j++) {    */
           xi[j][ibig]=xi[j][n];  }
           xi[j][n]=xit[j];  
         }  /*************************free ma3x ************************/
 #ifdef DEBUG  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  {
         for(j=1;j<=n;j++)    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
           printf(" %.12e",xit[j]);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         printf("\n");    free((FREE_ARG)(m+nrl-NR_END));
 #endif  }
       }  
     }  /*************** function subdirf ***********/
   }  char *subdirf(char fileres[])
 }  {
     /* Caution optionfilefiname is hidden */
 /**** Prevalence limit ****************/    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
 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 subdirf2 ***********/
   int i, ii,j,k;  char *subdirf2(char fileres[], char *preop)
   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,fileres);
     for (j=1;j<=nlstate+ndeath;j++){    return tmpout;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  }
     }  
   /*************** function subdirf3 ***********/
    cov[1]=1.;  char *subdirf3(char fileres[], char *preop, char *preop2)
    {
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    /* Caution optionfilefiname is hidden */
     newm=savm;    strcpy(tmpout,optionfilefiname);
     /* Covariates have to be included here again */    strcat(tmpout,"/");
      cov[2]=agefin;    strcat(tmpout,preop);
      strcat(tmpout,preop2);
       for (k=1; k<=cptcovn;k++) {    strcat(tmpout,fileres);
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    return tmpout;
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  }
       }  
       for (k=1; k<=cptcovage;k++)  /***************** f1dim *************************/
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  extern int ncom; 
       for (k=1; k<=cptcovprod;k++)  extern double *pcom,*xicom;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  extern double (*nrfunc)(double []); 
    
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  double f1dim(double x) 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  { 
     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)) 
     /*ps[3][2]=1;*/          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         else { 
   for(i=1; i<= nlstate; i++){          d=p/q; 
      s1=0;          u=x+d; 
     for(j=1; j<i; j++)          if (u-a < tol2 || b-u < tol2) 
       s1+=exp(ps[i][j]);            d=SIGN(tol1,xm-x); 
     for(j=i+1; j<=nlstate+ndeath; j++)        } 
       s1+=exp(ps[i][j]);      } else { 
     ps[i][i]=1./(s1+1.);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     for(j=1; j<i; j++)      } 
       ps[i][j]= exp(ps[i][j])*ps[i][i];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     for(j=i+1; j<=nlstate+ndeath; j++)      fu=(*f)(u); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];      if (fu <= fx) { 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        if (u >= x) a=x; else b=x; 
   } /* end i */        SHFT(v,w,x,u) 
           SHFT(fv,fw,fx,fu) 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){          } else { 
     for(jj=1; jj<= nlstate+ndeath; jj++){            if (u < x) a=u; else b=u; 
       ps[ii][jj]=0;            if (fu <= fw || w == x) { 
       ps[ii][ii]=1;              v=w; 
     }              w=u; 
   }              fv=fw; 
               fw=fu; 
             } else if (fu <= fv || v == x || v == w) { 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){              v=u; 
     for(jj=1; jj<= nlstate+ndeath; jj++){              fv=fu; 
      printf("%lf ",ps[ii][jj]);            } 
    }          } 
     printf("\n ");    } 
     }    nrerror("Too many iterations in brent"); 
     printf("\n ");printf("%lf ",cov[2]);*/    *xmin=x; 
 /*    return fx; 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  } 
   goto end;*/  
     return ps;  /****************** mnbrak ***********************/
 }  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
 /**************** Product of 2 matrices ******************/              double (*func)(double)) 
   { 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    double ulim,u,r,q, dum;
 {    double fu; 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times   
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    *fa=(*func)(*ax); 
   /* in, b, out are matrice of pointers which should have been initialized    *fb=(*func)(*bx); 
      before: only the contents of out is modified. The function returns    if (*fb > *fa) { 
      a pointer to pointers identical to out */      SHFT(dum,*ax,*bx,dum) 
   long i, j, k;        SHFT(dum,*fb,*fa,dum) 
   for(i=nrl; i<= nrh; i++)        } 
     for(k=ncolol; k<=ncoloh; k++)    *cx=(*bx)+GOLD*(*bx-*ax); 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    *fc=(*func)(*cx); 
         out[i][k] +=in[i][j]*b[j][k];    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
   return out;      q=(*bx-*cx)*(*fb-*fa); 
 }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
 /************* Higher Matrix Product ***************/      if ((*bx-u)*(u-*cx) > 0.0) { 
         fu=(*func)(u); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      } else if ((*cx-u)*(u-ulim) > 0.0) { 
 {        fu=(*func)(u); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        if (fu < *fc) { 
      duration (i.e. until          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.            SHFT(*fb,*fc,fu,(*func)(u)) 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step            } 
      (typically every 2 years instead of every month which is too big).      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
      Model is determined by parameters x and covariates have to be        u=ulim; 
      included manually here.        fu=(*func)(u); 
       } else { 
      */        u=(*cx)+GOLD*(*cx-*bx); 
         fu=(*func)(u); 
   int i, j, d, h, k;      } 
   double **out, cov[NCOVMAX];      SHFT(*ax,*bx,*cx,u) 
   double **newm;        SHFT(*fa,*fb,*fc,fu) 
         } 
   /* Hstepm could be zero and should return the unit matrix */  } 
   for (i=1;i<=nlstate+ndeath;i++)  
     for (j=1;j<=nlstate+ndeath;j++){  /*************** linmin ************************/
       oldm[i][j]=(i==j ? 1.0 : 0.0);  
       po[i][j][0]=(i==j ? 1.0 : 0.0);  int ncom; 
     }  double *pcom,*xicom;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  double (*nrfunc)(double []); 
   for(h=1; h <=nhstepm; h++){   
     for(d=1; d <=hstepm; d++){  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       newm=savm;  { 
       /* Covariates have to be included here again */    double brent(double ax, double bx, double cx, 
       cov[1]=1.;                 double (*f)(double), double tol, double *xmin); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    double f1dim(double x); 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       for (k=1; k<=cptcovage;k++)                double *fc, double (*func)(double)); 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    int j; 
       for (k=1; k<=cptcovprod;k++)    double xx,xmin,bx,ax; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    double fx,fb,fa;
    
     ncom=n; 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    pcom=vector(1,n); 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    xicom=vector(1,n); 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    nrfunc=func; 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    for (j=1;j<=n;j++) { 
       savm=oldm;      pcom[j]=p[j]; 
       oldm=newm;      xicom[j]=xi[j]; 
     }    } 
     for(i=1; i<=nlstate+ndeath; i++)    ax=0.0; 
       for(j=1;j<=nlstate+ndeath;j++) {    xx=1.0; 
         po[i][j][h]=newm[i][j];    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
          */  #ifdef DEBUG
       }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   } /* end h */    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   return po;  #endif
 }    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
       p[j] += xi[j]; 
 /*************** log-likelihood *************/    } 
 double func( double *x)    free_vector(xicom,1,n); 
 {    free_vector(pcom,1,n); 
   int i, ii, j, k, mi, d, kk;  } 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;  char *asc_diff_time(long time_sec, char ascdiff[])
   double sw; /* Sum of weights */  {
   double lli; /* Individual log likelihood */    long sec_left, days, hours, minutes;
   long ipmx;    days = (time_sec) / (60*60*24);
   /*extern weight */    sec_left = (time_sec) % (60*60*24);
   /* We are differentiating ll according to initial status */    hours = (sec_left) / (60*60) ;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    sec_left = (sec_left) %(60*60);
   /*for(i=1;i<imx;i++)    minutes = (sec_left) /60;
     printf(" %d\n",s[4][i]);    sec_left = (sec_left) % (60);
   */    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   cov[1]=1.;    return ascdiff;
   }
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  /*************** powell ************************/
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     for(mi=1; mi<= wav[i]-1; mi++){              double (*func)(double [])) 
       for (ii=1;ii<=nlstate+ndeath;ii++)  { 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    void linmin(double p[], double xi[], int n, double *fret, 
       for(d=0; d<dh[mi][i]; d++){                double (*func)(double [])); 
         newm=savm;    int i,ibig,j; 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    double del,t,*pt,*ptt,*xit;
         for (kk=1; kk<=cptcovage;kk++) {    double fp,fptt;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    double *xits;
         }    int niterf, itmp;
          
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    pt=vector(1,n); 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    ptt=vector(1,n); 
         savm=oldm;    xit=vector(1,n); 
         oldm=newm;    xits=vector(1,n); 
            *fret=(*func)(p); 
            for (j=1;j<=n;j++) pt[j]=p[j]; 
       } /* end mult */    for (*iter=1;;++(*iter)) { 
            fp=(*fret); 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      ibig=0; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      del=0.0; 
       ipmx +=1;      last_time=curr_time;
       sw += weight[i];      (void) gettimeofday(&curr_time,&tzp);
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      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);
     } /* end of wave */      /*    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);
   } /* end of individual */      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];     for (i=1;i<=n;i++) {
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        printf(" %d %.12f",i, p[i]);
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        fprintf(ficlog," %d %.12lf",i, p[i]);
   return -l;        fprintf(ficrespow," %.12lf", p[i]);
 }      }
       printf("\n");
       fprintf(ficlog,"\n");
 /*********** Maximum Likelihood Estimation ***************/      fprintf(ficrespow,"\n");fflush(ficrespow);
       if(*iter <=3){
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        tm = *localtime(&curr_time.tv_sec);
 {        strcpy(strcurr,asctime(&tm));
   int i,j, iter;  /*       asctime_r(&tm,strcurr); */
   double **xi,*delti;        forecast_time=curr_time; 
   double fret;        itmp = strlen(strcurr);
   xi=matrix(1,npar,1,npar);        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   for (i=1;i<=npar;i++)          strcurr[itmp-1]='\0';
     for (j=1;j<=npar;j++)        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       xi[i][j]=(i==j ? 1.0 : 0.0);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   printf("Powell\n");        for(niterf=10;niterf<=30;niterf+=10){
   powell(p,xi,npar,ftol,&iter,&fret,func);          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
           tmf = *localtime(&forecast_time.tv_sec);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  /*      asctime_r(&tmf,strfor); */
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));          strcpy(strfor,asctime(&tmf));
           itmp = strlen(strfor);
 }          if(strfor[itmp-1]=='\n')
           strfor[itmp-1]='\0';
 /**** Computes Hessian and covariance matrix ***/          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
 {        }
   double  **a,**y,*x,pd;      }
   double **hess;      for (i=1;i<=n;i++) { 
   int i, j,jk;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   int *indx;        fptt=(*fret); 
   #ifdef DEBUG
   double hessii(double p[], double delta, int theta, double delti[]);        printf("fret=%lf \n",*fret);
   double hessij(double p[], double delti[], int i, int j);        fprintf(ficlog,"fret=%lf \n",*fret);
   void lubksb(double **a, int npar, int *indx, double b[]) ;  #endif
   void ludcmp(double **a, int npar, int *indx, double *d) ;        printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
   hess=matrix(1,npar,1,npar);        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
   printf("\nCalculation of the hessian matrix. Wait...\n");          del=fabs(fptt-(*fret)); 
   for (i=1;i<=npar;i++){          ibig=i; 
     printf("%d",i);fflush(stdout);        } 
     hess[i][i]=hessii(p,ftolhess,i,delti);  #ifdef DEBUG
     /*printf(" %f ",p[i]);*/        printf("%d %.12e",i,(*fret));
     /*printf(" %lf ",hess[i][i]);*/        fprintf(ficlog,"%d %.12e",i,(*fret));
   }        for (j=1;j<=n;j++) {
            xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   for (i=1;i<=npar;i++) {          printf(" x(%d)=%.12e",j,xit[j]);
     for (j=1;j<=npar;j++)  {          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       if (j>i) {        }
         printf(".%d%d",i,j);fflush(stdout);        for(j=1;j<=n;j++) {
         hess[i][j]=hessij(p,delti,i,j);          printf(" p=%.12e",p[j]);
         hess[j][i]=hess[i][j];              fprintf(ficlog," p=%.12e",p[j]);
         /*printf(" %lf ",hess[i][j]);*/        }
       }        printf("\n");
     }        fprintf(ficlog,"\n");
   }  #endif
   printf("\n");      } 
       if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  #ifdef DEBUG
          int k[2],l;
   a=matrix(1,npar,1,npar);        k[0]=1;
   y=matrix(1,npar,1,npar);        k[1]=-1;
   x=vector(1,npar);        printf("Max: %.12e",(*func)(p));
   indx=ivector(1,npar);        fprintf(ficlog,"Max: %.12e",(*func)(p));
   for (i=1;i<=npar;i++)        for (j=1;j<=n;j++) {
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          printf(" %.12e",p[j]);
   ludcmp(a,npar,indx,&pd);          fprintf(ficlog," %.12e",p[j]);
         }
   for (j=1;j<=npar;j++) {        printf("\n");
     for (i=1;i<=npar;i++) x[i]=0;        fprintf(ficlog,"\n");
     x[j]=1;        for(l=0;l<=1;l++) {
     lubksb(a,npar,indx,x);          for (j=1;j<=n;j++) {
     for (i=1;i<=npar;i++){            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       matcov[i][j]=x[i];            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("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   printf("\n#Hessian matrix#\n");          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   for (i=1;i<=npar;i++) {        }
     for (j=1;j<=npar;j++) {  #endif
       printf("%.3e ",hess[i][j]);  
     }  
     printf("\n");        free_vector(xit,1,n); 
   }        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
   /* Recompute Inverse */        free_vector(pt,1,n); 
   for (i=1;i<=npar;i++)        return; 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      } 
   ludcmp(a,npar,indx,&pd);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
   /*  printf("\n#Hessian matrix recomputed#\n");        ptt[j]=2.0*p[j]-pt[j]; 
         xit[j]=p[j]-pt[j]; 
   for (j=1;j<=npar;j++) {        pt[j]=p[j]; 
     for (i=1;i<=npar;i++) x[i]=0;      } 
     x[j]=1;      fptt=(*func)(ptt); 
     lubksb(a,npar,indx,x);      if (fptt < fp) { 
     for (i=1;i<=npar;i++){        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       y[i][j]=x[i];        if (t < 0.0) { 
       printf("%.3e ",y[i][j]);          linmin(p,xit,n,fret,func); 
     }          for (j=1;j<=n;j++) { 
     printf("\n");            xi[j][ibig]=xi[j][n]; 
   }            xi[j][n]=xit[j]; 
   */          }
   #ifdef DEBUG
   free_matrix(a,1,npar,1,npar);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   free_matrix(y,1,npar,1,npar);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   free_vector(x,1,npar);          for(j=1;j<=n;j++){
   free_ivector(indx,1,npar);            printf(" %.12e",xit[j]);
   free_matrix(hess,1,npar,1,npar);            fprintf(ficlog," %.12e",xit[j]);
           }
           printf("\n");
 }          fprintf(ficlog,"\n");
   #endif
 /*************** hessian matrix ****************/        }
 double hessii( double x[], double delta, int theta, double delti[])      } 
 {    } 
   int i;  } 
   int l=1, lmax=20;  
   double k1,k2;  /**** Prevalence limit (stable prevalence)  ****************/
   double p2[NPARMAX+1];  
   double res;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  {
   double fx;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   int k=0,kmax=10;       matrix by transitions matrix until convergence is reached */
   double l1;  
     int i, ii,j,k;
   fx=func(x);    double min, max, maxmin, maxmax,sumnew=0.;
   for (i=1;i<=npar;i++) p2[i]=x[i];    double **matprod2();
   for(l=0 ; l <=lmax; l++){    double **out, cov[NCOVMAX], **pmij();
     l1=pow(10,l);    double **newm;
     delts=delt;    double agefin, delaymax=50 ; /* Max number of years to converge */
     for(k=1 ; k <kmax; k=k+1){  
       delt = delta*(l1*k);    for (ii=1;ii<=nlstate+ndeath;ii++)
       p2[theta]=x[theta] +delt;      for (j=1;j<=nlstate+ndeath;j++){
       k1=func(p2)-fx;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       p2[theta]=x[theta]-delt;      }
       k2=func(p2)-fx;  
       /*res= (k1-2.0*fx+k2)/delt/delt; */     cov[1]=1.;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */   
         /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 #ifdef DEBUG    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       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);      newm=savm;
 #endif      /* Covariates have to be included here again */
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */       cov[2]=agefin;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    
         k=kmax;        for (k=1; k<=cptcovn;k++) {
       }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          /*      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]]);*/
         k=kmax; l=lmax*10.;        }
       }        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        for (k=1; k<=cptcovprod;k++)
         delts=delt;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       }  
     }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   }        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   delti[theta]=delts;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   return res;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
    
 }      savm=oldm;
       oldm=newm;
 double hessij( double x[], double delti[], int thetai,int thetaj)      maxmax=0.;
 {      for(j=1;j<=nlstate;j++){
   int i;        min=1.;
   int l=1, l1, lmax=20;        max=0.;
   double k1,k2,k3,k4,res,fx;        for(i=1; i<=nlstate; i++) {
   double p2[NPARMAX+1];          sumnew=0;
   int k;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           prlim[i][j]= newm[i][j]/(1-sumnew);
   fx=func(x);          max=FMAX(max,prlim[i][j]);
   for (k=1; k<=2; k++) {          min=FMIN(min,prlim[i][j]);
     for (i=1;i<=npar;i++) p2[i]=x[i];        }
     p2[thetai]=x[thetai]+delti[thetai]/k;        maxmin=max-min;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        maxmax=FMAX(maxmax,maxmin);
     k1=func(p2)-fx;      }
        if(maxmax < ftolpl){
     p2[thetai]=x[thetai]+delti[thetai]/k;        return prlim;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      }
     k2=func(p2)-fx;    }
    }
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  /*************** transition probabilities ***************/ 
     k3=func(p2)-fx;  
    double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     p2[thetai]=x[thetai]-delti[thetai]/k;  {
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    double s1, s2;
     k4=func(p2)-fx;    /*double t34;*/
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    int i,j,j1, nc, ii, jj;
 #ifdef DEBUG  
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);      for(i=1; i<= nlstate; i++){
 #endif        for(j=1; j<i;j++){
   }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   return res;            /*s2 += param[i][j][nc]*cov[nc];*/
 }            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
 /************** Inverse of matrix **************/          }
 void ludcmp(double **a, int n, int *indx, double *d)          ps[i][j]=s2;
 {  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   int i,imax,j,k;        }
   double big,dum,sum,temp;        for(j=i+1; j<=nlstate+ndeath;j++){
   double *vv;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
              s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   vv=vector(1,n);  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
   *d=1.0;          }
   for (i=1;i<=n;i++) {          ps[i][j]=s2;
     big=0.0;        }
     for (j=1;j<=n;j++)      }
       if ((temp=fabs(a[i][j])) > big) big=temp;      /*ps[3][2]=1;*/
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      
     vv[i]=1.0/big;      for(i=1; i<= nlstate; i++){
   }        s1=0;
   for (j=1;j<=n;j++) {        for(j=1; j<i; j++)
     for (i=1;i<j;i++) {          s1+=exp(ps[i][j]);
       sum=a[i][j];        for(j=i+1; j<=nlstate+ndeath; j++)
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          s1+=exp(ps[i][j]);
       a[i][j]=sum;        ps[i][i]=1./(s1+1.);
     }        for(j=1; j<i; j++)
     big=0.0;          ps[i][j]= exp(ps[i][j])*ps[i][i];
     for (i=j;i<=n;i++) {        for(j=i+1; j<=nlstate+ndeath; j++)
       sum=a[i][j];          ps[i][j]= exp(ps[i][j])*ps[i][i];
       for (k=1;k<j;k++)        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         sum -= a[i][k]*a[k][j];      } /* end i */
       a[i][j]=sum;      
       if ( (dum=vv[i]*fabs(sum)) >= big) {      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         big=dum;        for(jj=1; jj<= nlstate+ndeath; jj++){
         imax=i;          ps[ii][jj]=0;
       }          ps[ii][ii]=1;
     }        }
     if (j != imax) {      }
       for (k=1;k<=n;k++) {      
         dum=a[imax][k];  
         a[imax][k]=a[j][k];  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
         a[j][k]=dum;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
       }  /*         printf("ddd %lf ",ps[ii][jj]); */
       *d = -(*d);  /*       } */
       vv[imax]=vv[j];  /*       printf("\n "); */
     }  /*        } */
     indx[j]=imax;  /*        printf("\n ");printf("%lf ",cov[2]); */
     if (a[j][j] == 0.0) a[j][j]=TINY;         /*
     if (j != n) {        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       dum=1.0/(a[j][j]);        goto end;*/
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      return ps;
     }  }
   }  
   free_vector(vv,1,n);  /* Doesn't work */  /**************** Product of 2 matrices ******************/
 ;  
 }  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   {
 void lubksb(double **a, int n, int *indx, double b[])    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
 {       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   int i,ii=0,ip,j;    /* in, b, out are matrice of pointers which should have been initialized 
   double sum;       before: only the contents of out is modified. The function returns
         a pointer to pointers identical to out */
   for (i=1;i<=n;i++) {    long i, j, k;
     ip=indx[i];    for(i=nrl; i<= nrh; i++)
     sum=b[ip];      for(k=ncolol; k<=ncoloh; k++)
     b[ip]=b[i];        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     if (ii)          out[i][k] +=in[i][j]*b[j][k];
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  
     else if (sum) ii=i;    return out;
     b[i]=sum;  }
   }  
   for (i=n;i>=1;i--) {  
     sum=b[i];  /************* Higher Matrix Product ***************/
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  
     b[i]=sum/a[i][i];  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   }  {
 }    /* Computes the transition matrix starting at age 'age' over 
        'nhstepm*hstepm*stepm' months (i.e. until
 /************ Frequencies ********************/       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1,double **mint,double **anint, int boolprev, double dateprev1,double dateprev2)       nhstepm*hstepm matrices. 
 {  /* Some frequencies */       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         (typically every 2 years instead of every month which is too big 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;       for the memory).
   double ***freq; /* Frequencies */       Model is determined by parameters x and covariates have to be 
   double *pp;       included manually here. 
   double pos, k2;  
   FILE *ficresp;       */
   char fileresp[FILENAMELENGTH];  
     int i, j, d, h, k;
   pp=vector(1,nlstate);    double **out, cov[NCOVMAX];
   probs= ma3x(1,130 ,1,8, 1,8);    double **newm;
   strcpy(fileresp,"p");  
   strcat(fileresp,fileres);    /* Hstepm could be zero and should return the unit matrix */
   if((ficresp=fopen(fileresp,"w"))==NULL) {    for (i=1;i<=nlstate+ndeath;i++)
     printf("Problem with prevalence resultfile: %s\n", fileresp);      for (j=1;j<=nlstate+ndeath;j++){
     exit(0);        oldm[i][j]=(i==j ? 1.0 : 0.0);
   }        po[i][j][0]=(i==j ? 1.0 : 0.0);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      }
   j1=0;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
   j=cptcoveff;      for(d=1; d <=hstepm; d++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        newm=savm;
         /* Covariates have to be included here again */
   for(k1=1; k1<=j;k1++){        cov[1]=1.;
    for(i1=1; i1<=ncodemax[k1];i1++){        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
        j1++;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        for (k=1; k<=cptcovage;k++)
          scanf("%d", i);*/          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (i=-1; i<=nlstate+ndeath; i++)          for (k=1; k<=cptcovprod;k++)
          for (jk=-1; jk<=nlstate+ndeath; jk++)            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
            for(m=agemin; m <= agemax+3; m++)  
              freq[i][jk][m]=0;  
                /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
        for (i=1; i<=imx; i++) {        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
          bool=1;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
          if  (cptcovn>0) {                     pmij(pmmij,cov,ncovmodel,x,nlstate));
            for (z1=1; z1<=cptcoveff; z1++)        savm=oldm;
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        oldm=newm;
                bool=0;      }
          }      for(i=1; i<=nlstate+ndeath; i++)
          if (bool==1) {        for(j=1;j<=nlstate+ndeath;j++) {
            if (boolprev==1){          po[i][j][h]=newm[i][j];
              for(m=fprev1; m<=lprev1; m++){          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
                if(agev[m][i]==0) agev[m][i]=agemax+1;           */
                if(agev[m][i]==1) agev[m][i]=agemax+2;        }
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    } /* end h */
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    return po;
              }  }
            }  
            else {  
             for(m=firstpass; m<=lastpass; m++){  /*************** log-likelihood *************/
              k2=anint[m][i]+(mint[m][i]/12.);  double func( double *x)
              if ((k2>=dateprev1) && (k2<=dateprev2)) {  {
              if(agev[m][i]==0) agev[m][i]=agemax+1;    int i, ii, j, k, mi, d, kk;
              if(agev[m][i]==1) agev[m][i]=agemax+2;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    double **out;
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    double sw; /* Sum of weights */
              }    double lli; /* Individual log likelihood */
             }    int s1, s2;
            }    double bbh, survp;
           }    long ipmx;
        }    /*extern weight */
         if  (cptcovn>0) {    /* We are differentiating ll according to initial status */
          fprintf(ficresp, "\n#********** Variable ");    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    /*for(i=1;i<imx;i++) 
        fprintf(ficresp, "**********\n#");      printf(" %d\n",s[4][i]);
         }    */
        for(i=1; i<=nlstate;i++)    cov[1]=1.;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  
        fprintf(ficresp, "\n");    for(k=1; k<=nlstate; k++) ll[k]=0.;
          
   for(i=(int)agemin; i <= (int)agemax+3; i++){    if(mle==1){
     if(i==(int)agemax+3)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       printf("Total");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     else        for(mi=1; mi<= wav[i]-1; mi++){
       printf("Age %d", i);          for (ii=1;ii<=nlstate+ndeath;ii++)
     for(jk=1; jk <=nlstate ; jk++){            for (j=1;j<=nlstate+ndeath;j++){
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         pp[jk] += freq[jk][m][i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }            }
     for(jk=1; jk <=nlstate ; jk++){          for(d=0; d<dh[mi][i]; d++){
       for(m=-1, pos=0; m <=0 ; m++)            newm=savm;
         pos += freq[jk][m][i];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if(pp[jk]>=1.e-10)            for (kk=1; kk<=cptcovage;kk++) {
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       else            }
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
      for(jk=1; jk <=nlstate ; jk++){            oldm=newm;
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          } /* end mult */
         pp[jk] += freq[jk][m][i];        
      }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias at large stepm.
     for(jk=1,pos=0; jk <=nlstate ; jk++)           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       pos += pp[jk];           * (in months) between two waves is not a multiple of stepm, we rounded to 
     for(jk=1; jk <=nlstate ; jk++){           * the nearest (and in case of equal distance, to the lowest) interval but now
       if(pos>=1.e-5)           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
       else           * probability in order to take into account the bias as a fraction of the way
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
       if( i <= (int) agemax){           * -stepm/2 to stepm/2 .
         if(pos>=1.e-5){           * For stepm=1 the results are the same as for previous versions of Imach.
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);           * For stepm > 1 the results are less biased than in previous versions. 
           probs[i][jk][j1]= pp[jk]/pos;           */
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
       else          bbh=(double)bh[mi][i]/(double)stepm; 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          /* bias bh is positive if real duration
       }           * is higher than the multiple of stepm and negative otherwise.
     }           */
     for(jk=-1; jk <=nlstate+ndeath; jk++)          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       for(m=-1; m <=nlstate+ndeath; m++)          if( s2 > nlstate){ 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            /* i.e. if s2 is a death state and if the date of death is known then the contribution
     if(i <= (int) agemax)               to the likelihood is the probability to die between last step unit time and current 
       fprintf(ficresp,"\n");               step unit time, which is also equal to probability to die before dh 
     printf("\n");               minus probability to die before dh-stepm . 
     }               In version up to 0.92 likelihood was computed
     }          as if date of death was unknown. Death was treated as any other
  }          health state: the date of the interview describes the actual state
            and not the date of a change in health state. The former idea was
   fclose(ficresp);          to consider that at each interview the state was recorded
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          (healthy, disable or death) and IMaCh was corrected; but when we
   free_vector(pp,1,nlstate);          introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
 }  /* End of Freq */          contribution is smaller and very dependent of the step unit
           stepm. It is no more the probability to die between last interview
 /************ Prevalence ********************/          and month of death but the probability to survive from last
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1, double **mint,double **anint,int boolprev, double dateprev1, double dateprev2)          interview up to one month before death multiplied by the
 {  /* Some frequencies */          probability to die within a month. Thanks to Chris
            Jackson for correcting this bug.  Former versions increased
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          mortality artificially. The bad side is that we add another loop
   double ***freq; /* Frequencies */          which slows down the processing. The difference can be up to 10%
   double *pp;          lower mortality.
   double pos, k2;            */
             lli=log(out[s1][s2] - savm[s1][s2]);
   pp=vector(1,nlstate);          }else{
   probs= ma3x(1,130 ,1,8, 1,8);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
              /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          } 
   j1=0;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
            /*if(lli ==000.0)*/
   j=cptcoveff;          /*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); */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          ipmx +=1;
            sw += weight[i];
  for(k1=1; k1<=j;k1++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(i1=1; i1<=ncodemax[k1];i1++){        } /* end of wave */
       j1++;      } /* end of individual */
      }  else if(mle==2){
       for (i=-1; i<=nlstate+ndeath; i++)        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (jk=-1; jk<=nlstate+ndeath; jk++)          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           for(m=agemin; m <= agemax+3; m++)        for(mi=1; mi<= wav[i]-1; mi++){
           freq[i][jk][m]=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
                  for (j=1;j<=nlstate+ndeath;j++){
       for (i=1; i<=imx; i++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         bool=1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         if  (cptcovn>0) {            }
           for (z1=1; z1<=cptcoveff; z1++)          for(d=0; d<=dh[mi][i]; d++){
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            newm=savm;
               bool=0;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
               }            for (kk=1; kk<=cptcovage;kk++) {
         if (bool==1) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           if (boolprev==1){            }
             for(m=fprev1; m<=lprev1; m++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
               if(agev[m][i]==0) agev[m][i]=agemax+1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               if(agev[m][i]==1) agev[m][i]=agemax+2;            savm=oldm;
               freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];            oldm=newm;
               freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          } /* end mult */
             }        
           }          s1=s[mw[mi][i]][i];
           else {          s2=s[mw[mi+1][i]][i];
             for(m=firstpass; m<=lastpass; m++){          bbh=(double)bh[mi][i]/(double)stepm; 
               k2=anint[m][i]+(mint[m][i]/12.);          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 ((k2>=dateprev1) && (k2<=dateprev2)) {          ipmx +=1;
                 if(agev[m][i]==0) agev[m][i]=agemax+1;          sw += weight[i];
                 if(agev[m][i]==1) agev[m][i]=agemax+2;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        } /* end of wave */
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      } /* end of individual */
               }    }  else if(mle==3){  /* exponential inter-extrapolation */
             }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
         for(i=(int)agemin; i <= (int)agemax+3; i++){            for (j=1;j<=nlstate+ndeath;j++){
           for(jk=1; jk <=nlstate ; jk++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
               pp[jk] += freq[jk][m][i];            }
           }          for(d=0; d<dh[mi][i]; d++){
           for(jk=1; jk <=nlstate ; jk++){            newm=savm;
             for(m=-1, pos=0; m <=0 ; m++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             pos += freq[jk][m][i];            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                    }
          for(jk=1; jk <=nlstate ; jk++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              pp[jk] += freq[jk][m][i];            savm=oldm;
          }            oldm=newm;
                    } /* end mult */
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        
           s1=s[mw[mi][i]][i];
          for(jk=1; jk <=nlstate ; jk++){                    s2=s[mw[mi+1][i]][i];
            if( i <= (int) agemax){          bbh=(double)bh[mi][i]/(double)stepm; 
              if(pos>=1.e-5){          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 */
                probs[i][jk][j1]= pp[jk]/pos;          ipmx +=1;
              }          sw += weight[i];
            }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          }        } /* end of wave */
                } /* end of individual */
         }    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            for (j=1;j<=nlstate+ndeath;j++){
   free_vector(pp,1,nlstate);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }  /* End of Freq */            }
 /************* Waves Concatenation ***************/          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 {            for (kk=1; kk<=cptcovage;kk++) {
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      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          
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      and mw[mi+1][i]. dh depends on stepm.                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      */            savm=oldm;
             oldm=newm;
   int i, mi, m;          } /* end mult */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        
      double sum=0., jmean=0.;*/          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
   int j, k=0,jk, ju, jl;          if( s2 > nlstate){ 
   double sum=0.;            lli=log(out[s1][s2] - savm[s1][s2]);
   jmin=1e+5;          }else{
   jmax=-1;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   jmean=0.;          }
   for(i=1; i<=imx; i++){          ipmx +=1;
     mi=0;          sw += weight[i];
     m=firstpass;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     while(s[m][i] <= nlstate){  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       if(s[m][i]>=1)        } /* end of wave */
         mw[++mi][i]=m;      } /* end of individual */
       if(m >=lastpass)    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
         break;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       else        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         m++;        for(mi=1; mi<= wav[i]-1; mi++){
     }/* end while */          for (ii=1;ii<=nlstate+ndeath;ii++)
     if (s[m][i] > nlstate){            for (j=1;j<=nlstate+ndeath;j++){
       mi++;     /* Death is another wave */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       /* if(mi==0)  never been interviewed correctly before death */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
          /* Only death is a correct wave */            }
       mw[mi][i]=m;          for(d=0; d<dh[mi][i]; d++){
     }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     wav[i]=mi;            for (kk=1; kk<=cptcovage;kk++) {
     if(mi==0)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            }
   }          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for(i=1; i<=imx; i++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(mi=1; mi<wav[i];mi++){            savm=oldm;
       if (stepm <=0)            oldm=newm;
         dh[mi][i]=1;          } /* end mult */
       else{        
         if (s[mw[mi+1][i]][i] > nlstate) {          s1=s[mw[mi][i]][i];
           if (agedc[i] < 2*AGESUP) {          s2=s[mw[mi+1][i]][i];
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           if(j==0) j=1;  /* Survives at least one month after exam */          ipmx +=1;
           k=k+1;          sw += weight[i];
           if (j >= jmax) jmax=j;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           if (j <= jmin) jmin=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]);*/
           sum=sum+j;        } /* end of wave */
           /* if (j<10) printf("j=%d num=%d ",j,i); */      } /* end of individual */
           }    } /* End of if */
         }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         else{    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           k=k+1;    return -l;
           if (j >= jmax) jmax=j;  }
           else if (j <= jmin)jmin=j;  
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  /*************** log-likelihood *************/
           sum=sum+j;  double funcone( double *x)
         }  {
         jk= j/stepm;    /* Same as likeli but slower because of a lot of printf and if */
         jl= j -jk*stepm;    int i, ii, j, k, mi, d, kk;
         ju= j -(jk+1)*stepm;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         if(jl <= -ju)    double **out;
           dh[mi][i]=jk;    double lli; /* Individual log likelihood */
         else    double llt;
           dh[mi][i]=jk+1;    int s1, s2;
         if(dh[mi][i]==0)    double bbh, survp;
           dh[mi][i]=1; /* At least one step */    /*extern weight */
       }    /* We are differentiating ll according to initial status */
     }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   }    /*for(i=1;i<imx;i++) 
   jmean=sum/k;      printf(" %d\n",s[4][i]);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    */
  }    cov[1]=1.;
 /*********** Tricode ****************************/  
 void tricode(int *Tvar, int **nbcode, int imx)    for(k=1; k<=nlstate; k++) ll[k]=0.;
 {  
   int Ndum[20],ij=1, k, j, i;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int cptcode=0;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   cptcoveff=0;      for(mi=1; mi<= wav[i]-1; mi++){
          for (ii=1;ii<=nlstate+ndeath;ii++)
   for (k=0; k<19; k++) Ndum[k]=0;          for (j=1;j<=nlstate+ndeath;j++){
   for (k=1; k<=7; k++) ncodemax[k]=0;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          }
     for (i=1; i<=imx; i++) {        for(d=0; d<dh[mi][i]; d++){
       ij=(int)(covar[Tvar[j]][i]);          newm=savm;
       Ndum[ij]++;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          for (kk=1; kk<=cptcovage;kk++) {
       if (ij > cptcode) cptcode=ij;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     }          }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for (i=0; i<=cptcode; i++) {                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       if(Ndum[i]!=0) ncodemax[j]++;          savm=oldm;
     }          oldm=newm;
     ij=1;        } /* end mult */
         
         s1=s[mw[mi][i]][i];
     for (i=1; i<=ncodemax[j]; i++) {        s2=s[mw[mi+1][i]][i];
       for (k=0; k<=19; k++) {        bbh=(double)bh[mi][i]/(double)stepm; 
         if (Ndum[k] != 0) {        /* bias is positive if real duration
           nbcode[Tvar[j]][ij]=k;         * is higher than the multiple of stepm and negative otherwise.
           ij++;         */
         }        if( s2 > nlstate && (mle <5) ){  /* Jackson */
         if (ij > ncodemax[j]) break;          lli=log(out[s1][s2] - savm[s1][s2]);
       }          } else if (mle==1){
     }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   }          } else if(mle==2){
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
  for (k=0; k<19; k++) Ndum[k]=0;        } else if(mle==3){  /* exponential inter-extrapolation */
           lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
  for (i=1; i<=ncovmodel-2; i++) {        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       ij=Tvar[i];          lli=log(out[s1][s2]); /* Original formula */
       Ndum[ij]++;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
     }          lli=log(out[s1][s2]); /* Original formula */
         } /* End of if */
  ij=1;        ipmx +=1;
  for (i=1; i<=10; i++) {        sw += weight[i];
    if((Ndum[i]!=0) && (i<=ncov)){        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      Tvaraff[ij]=i;  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
      ij++;        if(globpr){
    }          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
  }   %10.6f %10.6f %10.6f ", \
                    num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     cptcoveff=ij-1;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
 }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             llt +=ll[k]*gipmx/gsw;
 /*********** Health Expectancies ****************/            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          fprintf(ficresilk," %10.6f\n", -llt);
 {        }
   /* Health expectancies */      } /* end of wave */
   int i, j, nhstepm, hstepm, h;    } /* end of individual */
   double age, agelim,hf;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   double ***p3mat;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
      l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   fprintf(ficreseij,"# Health expectancies\n");    if(globpr==0){ /* First time we count the contributions and weights */
   fprintf(ficreseij,"# Age");      gipmx=ipmx;
   for(i=1; i<=nlstate;i++)      gsw=sw;
     for(j=1; j<=nlstate;j++)    }
       fprintf(ficreseij," %1d-%1d",i,j);    return -l;
   fprintf(ficreseij,"\n");  }
   
   hstepm=1*YEARM; /*  Every j years of age (in month) */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   agelim=AGESUP;  {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /* This routine should help understanding what is done with 
     /* nhstepm age range expressed in number of stepm */       the selection of individuals/waves and
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);       to check the exact contribution to the likelihood.
     /* Typically if 20 years = 20*12/6=40 stepm */       Plotting could be done.
     if (stepm >= YEARM) hstepm=1;     */
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    int k;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    if(*globpri !=0){ /* Just counts and sums, no printings */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      strcpy(fileresilk,"ilk"); 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
     for(i=1; i<=nlstate;i++)        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       for(j=1; j<=nlstate;j++)      }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){      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");
           eij[i][j][(int)age] +=p3mat[i][j][h];      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
         }      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
          for(k=1; k<=nlstate; k++) 
     hf=1;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     if (stepm >= YEARM) hf=stepm/YEARM;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     fprintf(ficreseij,"%.0f",age );    }
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){    *fretone=(*funcone)(p);
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);    if(*globpri !=0){
       }      fclose(ficresilk);
     fprintf(ficreseij,"\n");      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fflush(fichtm); 
   }    } 
 }    return;
   }
 /************ Variance ******************/  
 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)  
 {  /*********** Maximum Likelihood Estimation ***************/
   /* Variance of health expectancies */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   double **newm;  {
   double **dnewm,**doldm;    int i,j, iter;
   int i, j, nhstepm, hstepm, h;    double **xi;
   int k, cptcode;    double fret;
   double *xp;    double fretone; /* Only one call to likelihood */
   double **gp, **gm;    /*  char filerespow[FILENAMELENGTH];*/
   double ***gradg, ***trgradg;    xi=matrix(1,npar,1,npar);
   double ***p3mat;    for (i=1;i<=npar;i++)
   double age,agelim;      for (j=1;j<=npar;j++)
   int theta;        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
    fprintf(ficresvij,"# Covariances of life expectancies\n");    strcpy(filerespow,"pow"); 
   fprintf(ficresvij,"# Age");    strcat(filerespow,fileres);
   for(i=1; i<=nlstate;i++)    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     for(j=1; j<=nlstate;j++)      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   fprintf(ficresvij,"\n");    }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
   xp=vector(1,npar);    for (i=1;i<=nlstate;i++)
   dnewm=matrix(1,nlstate,1,npar);      for(j=1;j<=nlstate+ndeath;j++)
   doldm=matrix(1,nlstate,1,nlstate);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
      fprintf(ficrespow,"\n");
   hstepm=1*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    powell(p,xi,npar,ftol,&iter,&fret,func);
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    fclose(ficrespow);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     if (stepm >= YEARM) hstepm=1;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  }
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);  /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     for(theta=1; theta <=npar; theta++){  {
       for(i=1; i<=npar; i++){ /* Computes gradient */    double  **a,**y,*x,pd;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double **hess;
       }    int i, j,jk;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int *indx;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
     double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
       if (popbased==1) {    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
         for(i=1; i<=nlstate;i++)    void lubksb(double **a, int npar, int *indx, double b[]) ;
           prlim[i][i]=probs[(int)age][i][ij];    void ludcmp(double **a, int npar, int *indx, double *d) ;
       }    double gompertz(double p[]);
          hess=matrix(1,npar,1,npar);
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){    printf("\nCalculation of the hessian matrix. Wait...\n");
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    for (i=1;i<=npar;i++){
         }      printf("%d",i);fflush(stdout);
       }      fprintf(ficlog,"%d",i);fflush(ficlog);
         
       for(i=1; i<=npar; i++) /* Computes gradient */       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        /*  printf(" %f ",p[i]);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }
       if (popbased==1) {    
         for(i=1; i<=nlstate;i++)    for (i=1;i<=npar;i++) {
           prlim[i][i]=probs[(int)age][i][ij];      for (j=1;j<=npar;j++)  {
       }        if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
       for(j=1; j<= nlstate; j++){          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         for(h=0; h<=nhstepm; h++){          hess[i][j]=hessij(p,delti,i,j,func,npar);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          hess[j][i]=hess[i][j];    
         }          /*printf(" %lf ",hess[i][j]);*/
       }        }
       }
       for(j=1; j<= nlstate; j++)    }
         for(h=0; h<=nhstepm; h++){    printf("\n");
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    fprintf(ficlog,"\n");
         }  
     } /* End theta */    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    
     a=matrix(1,npar,1,npar);
     for(h=0; h<=nhstepm; h++)    y=matrix(1,npar,1,npar);
       for(j=1; j<=nlstate;j++)    x=vector(1,npar);
         for(theta=1; theta <=npar; theta++)    indx=ivector(1,npar);
           trgradg[h][j][theta]=gradg[h][theta][j];    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     for(i=1;i<=nlstate;i++)    ludcmp(a,npar,indx,&pd);
       for(j=1;j<=nlstate;j++)  
         vareij[i][j][(int)age] =0.;    for (j=1;j<=npar;j++) {
     for(h=0;h<=nhstepm;h++){      for (i=1;i<=npar;i++) x[i]=0;
       for(k=0;k<=nhstepm;k++){      x[j]=1;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      lubksb(a,npar,indx,x);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      for (i=1;i<=npar;i++){ 
         for(i=1;i<=nlstate;i++)        matcov[i][j]=x[i];
           for(j=1;j<=nlstate;j++)      }
             vareij[i][j][(int)age] += doldm[i][j];    }
       }  
     }    printf("\n#Hessian matrix#\n");
     h=1;    fprintf(ficlog,"\n#Hessian matrix#\n");
     if (stepm >= YEARM) h=stepm/YEARM;    for (i=1;i<=npar;i++) { 
     fprintf(ficresvij,"%.0f ",age );      for (j=1;j<=npar;j++) { 
     for(i=1; i<=nlstate;i++)        printf("%.3e ",hess[i][j]);
       for(j=1; j<=nlstate;j++){        fprintf(ficlog,"%.3e ",hess[i][j]);
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);      }
       }      printf("\n");
     fprintf(ficresvij,"\n");      fprintf(ficlog,"\n");
     free_matrix(gp,0,nhstepm,1,nlstate);    }
     free_matrix(gm,0,nhstepm,1,nlstate);  
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    /* Recompute Inverse */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    for (i=1;i<=npar;i++)
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   } /* End age */    ludcmp(a,npar,indx,&pd);
    
   free_vector(xp,1,npar);    /*  printf("\n#Hessian matrix recomputed#\n");
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
 }      x[j]=1;
       lubksb(a,npar,indx,x);
 /************ Variance of prevlim ******************/      for (i=1;i<=npar;i++){ 
 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)        y[i][j]=x[i];
 {        printf("%.3e ",y[i][j]);
   /* Variance of prevalence limit */        fprintf(ficlog,"%.3e ",y[i][j]);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      }
   double **newm;      printf("\n");
   double **dnewm,**doldm;      fprintf(ficlog,"\n");
   int i, j, nhstepm, hstepm;    }
   int k, cptcode;    */
   double *xp;  
   double *gp, *gm;    free_matrix(a,1,npar,1,npar);
   double **gradg, **trgradg;    free_matrix(y,1,npar,1,npar);
   double age,agelim;    free_vector(x,1,npar);
   int theta;    free_ivector(indx,1,npar);
        free_matrix(hess,1,npar,1,npar);
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");  
   fprintf(ficresvpl,"# Age");  
   for(i=1; i<=nlstate;i++)  }
       fprintf(ficresvpl," %1d-%1d",i,i);  
   fprintf(ficresvpl,"\n");  /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   xp=vector(1,npar);  {
   dnewm=matrix(1,nlstate,1,npar);    int i;
   doldm=matrix(1,nlstate,1,nlstate);    int l=1, lmax=20;
      double k1,k2;
   hstepm=1*YEARM; /* Every year of age */    double p2[NPARMAX+1];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    double res;
   agelim = AGESUP;    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double fx;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    int k=0,kmax=10;
     if (stepm >= YEARM) hstepm=1;    double l1;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
     gradg=matrix(1,npar,1,nlstate);    fx=func(x);
     gp=vector(1,nlstate);    for (i=1;i<=npar;i++) p2[i]=x[i];
     gm=vector(1,nlstate);    for(l=0 ; l <=lmax; l++){
       l1=pow(10,l);
     for(theta=1; theta <=npar; theta++){      delts=delt;
       for(i=1; i<=npar; i++){ /* Computes gradient */      for(k=1 ; k <kmax; k=k+1){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        delt = delta*(l1*k);
       }        p2[theta]=x[theta] +delt;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        k1=func(p2)-fx;
       for(i=1;i<=nlstate;i++)        p2[theta]=x[theta]-delt;
         gp[i] = prlim[i][i];        k2=func(p2)-fx;
            /*res= (k1-2.0*fx+k2)/delt/delt; */
       for(i=1; i<=npar; i++) /* Computes gradient */        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  #ifdef DEBUG
       for(i=1;i<=nlstate;i++)        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);
         gm[i] = prlim[i][i];        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   #endif
       for(i=1;i<=nlstate;i++)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     } /* End theta */          k=kmax;
         }
     trgradg =matrix(1,nlstate,1,npar);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10.;
     for(j=1; j<=nlstate;j++)        }
       for(theta=1; theta <=npar; theta++)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         trgradg[j][theta]=gradg[theta][j];          delts=delt;
         }
     for(i=1;i<=nlstate;i++)      }
       varpl[i][(int)age] =0.;    }
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    delti[theta]=delts;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    return res; 
     for(i=1;i<=nlstate;i++)    
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  }
   
     fprintf(ficresvpl,"%.0f ",age );  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     for(i=1; i<=nlstate;i++)  {
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    int i;
     fprintf(ficresvpl,"\n");    int l=1, l1, lmax=20;
     free_vector(gp,1,nlstate);    double k1,k2,k3,k4,res,fx;
     free_vector(gm,1,nlstate);    double p2[NPARMAX+1];
     free_matrix(gradg,1,npar,1,nlstate);    int k;
     free_matrix(trgradg,1,nlstate,1,npar);  
   } /* End age */    fx=func(x);
     for (k=1; k<=2; k++) {
   free_vector(xp,1,npar);      for (i=1;i<=npar;i++) p2[i]=x[i];
   free_matrix(doldm,1,nlstate,1,npar);      p2[thetai]=x[thetai]+delti[thetai]/k;
   free_matrix(dnewm,1,nlstate,1,nlstate);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k1=func(p2)-fx;
 }    
       p2[thetai]=x[thetai]+delti[thetai]/k;
 /************ Variance of one-step probabilities  ******************/      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)      k2=func(p2)-fx;
 {    
   int i, j;      p2[thetai]=x[thetai]-delti[thetai]/k;
   int k=0, cptcode;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double **dnewm,**doldm;      k3=func(p2)-fx;
   double *xp;    
   double *gp, *gm;      p2[thetai]=x[thetai]-delti[thetai]/k;
   double **gradg, **trgradg;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   double age,agelim, cov[NCOVMAX];      k4=func(p2)-fx;
   int theta;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   char fileresprob[FILENAMELENGTH];  #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);
   strcpy(fileresprob,"prob");      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);
   strcat(fileresprob,fileres);  #endif
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    }
     printf("Problem with resultfile: %s\n", fileresprob);    return res;
   }  }
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);  
    /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
   xp=vector(1,npar);  { 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    int i,imax,j,k; 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    double big,dum,sum,temp; 
      double *vv; 
   cov[1]=1;   
   for (age=bage; age<=fage; age ++){    vv=vector(1,n); 
     cov[2]=age;    *d=1.0; 
     gradg=matrix(1,npar,1,9);    for (i=1;i<=n;i++) { 
     trgradg=matrix(1,9,1,npar);      big=0.0; 
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      for (j=1;j<=n;j++) 
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        if ((temp=fabs(a[i][j])) > big) big=temp; 
          if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     for(theta=1; theta <=npar; theta++){      vv[i]=1.0/big; 
       for(i=1; i<=npar; i++)    } 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    for (j=1;j<=n;j++) { 
            for (i=1;i<j;i++) { 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        sum=a[i][j]; 
            for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       k=0;        a[i][j]=sum; 
       for(i=1; i<= (nlstate+ndeath); i++){      } 
         for(j=1; j<=(nlstate+ndeath);j++){      big=0.0; 
            k=k+1;      for (i=j;i<=n;i++) { 
           gp[k]=pmmij[i][j];        sum=a[i][j]; 
         }        for (k=1;k<j;k++) 
       }          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
       for(i=1; i<=npar; i++)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          big=dum; 
              imax=i; 
         } 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      } 
       k=0;      if (j != imax) { 
       for(i=1; i<=(nlstate+ndeath); i++){        for (k=1;k<=n;k++) { 
         for(j=1; j<=(nlstate+ndeath);j++){          dum=a[imax][k]; 
           k=k+1;          a[imax][k]=a[j][k]; 
           gm[k]=pmmij[i][j];          a[j][k]=dum; 
         }        } 
       }        *d = -(*d); 
              vv[imax]=vv[j]; 
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)      } 
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        indx[j]=imax; 
     }      if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)        dum=1.0/(a[j][j]); 
       for(theta=1; theta <=npar; theta++)        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       trgradg[j][theta]=gradg[theta][j];      } 
      } 
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    free_vector(vv,1,n);  /* Doesn't work */
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);  ;
   } 
      pmij(pmmij,cov,ncovmodel,x,nlstate);  
   void lubksb(double **a, int n, int *indx, double b[]) 
      k=0;  { 
      for(i=1; i<=(nlstate+ndeath); i++){    int i,ii=0,ip,j; 
        for(j=1; j<=(nlstate+ndeath);j++){    double sum; 
          k=k+1;   
          gm[k]=pmmij[i][j];    for (i=1;i<=n;i++) { 
         }      ip=indx[i]; 
      }      sum=b[ip]; 
            b[ip]=b[i]; 
      /*printf("\n%d ",(int)age);      if (ii) 
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
              else if (sum) ii=i; 
       b[i]=sum; 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    } 
      }*/    for (i=n;i>=1;i--) { 
       sum=b[i]; 
   fprintf(ficresprob,"\n%d ",(int)age);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       b[i]=sum/a[i][i]; 
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    } 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  } 
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  
   }  /************ 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)
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  {  /* Some frequencies */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    int first;
 }    double ***freq; /* Frequencies */
  free_vector(xp,1,npar);    double *pp, **prop;
 fclose(ficresprob);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
  exit(0);    FILE *ficresp;
 }    char fileresp[FILENAMELENGTH];
     
 /***********************************************/    pp=vector(1,nlstate);
 /**************** Main Program *****************/    prop=matrix(1,nlstate,iagemin,iagemax+3);
 /***********************************************/    strcpy(fileresp,"p");
     strcat(fileresp,fileres);
 /*int main(int argc, char *argv[])*/    if((ficresp=fopen(fileresp,"w"))==NULL) {
 int main()      printf("Problem with prevalence resultfile: %s\n", fileresp);
 {      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       exit(0);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    }
   double agedeb, agefin,hf;    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
   double agemin=1.e20, agemax=-1.e20;    j1=0;
     
   double fret;    j=cptcoveff;
   double **xi,tmp,delta;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
   double dum; /* Dummy variable */    first=1;
   double ***p3mat;  
   int *indx;    for(k1=1; k1<=j;k1++){
   char line[MAXLINE], linepar[MAXLINE];      for(i1=1; i1<=ncodemax[k1];i1++){
   char title[MAXLINE];        j1++;
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];          scanf("%d", i);*/
   char filerest[FILENAMELENGTH];        for (i=-1; i<=nlstate+ndeath; i++)  
   char fileregp[FILENAMELENGTH];          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   char popfile[FILENAMELENGTH];            for(m=iagemin; m <= iagemax+3; m++)
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];              freq[i][jk][m]=0;
   int firstobs=1, lastobs=10;  
   int sdeb, sfin; /* Status at beginning and end */      for (i=1; i<=nlstate; i++)  
   int c,  h , cpt,l;        for(m=iagemin; m <= iagemax+3; m++)
   int ju,jl, mi;          prop[i][m]=0;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        dateintsum=0;
   int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast,popforecast=0;        k2cpt=0;
   int hstepm, nhstepm;        for (i=1; i<=imx; i++) {
   int *popage,boolprev=0;/*boolprev=0 if date and zero if wave*/          bool=1;
           if  (cptcovn>0) {
   double bage, fage, age, agelim, agebase;            for (z1=1; z1<=cptcoveff; z1++) 
   double ftolpl=FTOL;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   double **prlim;                bool=0;
   double *severity;          }
   double ***param; /* Matrix of parameters */          if (bool==1){
   double  *p;            for(m=firstpass; m<=lastpass; m++){
   double **matcov; /* Matrix of covariance */              k2=anint[m][i]+(mint[m][i]/12.);
   double ***delti3; /* Scale */              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   double *delti; /* Scale */                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   double ***eij, ***vareij;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   double **varpl; /* Variances of prevalence limits by age */                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   double *epj, vepp;                if (m<lastpass) {
   double kk1, kk2;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   double *popeffectif,*popcount;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   double dateprev1, dateprev2;                }
                 
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   char *alph[]={"a","a","b","c","d","e"}, str[4];                  dateintsum=dateintsum+k2;
                   k2cpt++;
                 }
   char z[1]="c", occ;                /*}*/
 #include <sys/time.h>            }
 #include <time.h>          }
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        }
   char strfprev[10], strlprev[10];         
   char strfprevfore[10], strlprevfore[10];        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   /* long total_usecs;  
   struct timeval start_time, end_time;        if  (cptcovn>0) {
            fprintf(ficresp, "\n#********** Variable "); 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\n#");
         }
   printf("\nIMACH, Version 0.7");        for(i=1; i<=nlstate;i++) 
   printf("\nEnter the parameter file name: ");          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresp, "\n");
 #ifdef windows        
   scanf("%s",pathtot);        for(i=iagemin; i <= iagemax+3; i++){
   getcwd(pathcd, size);          if(i==iagemax+3){
   /*cygwin_split_path(pathtot,path,optionfile);            fprintf(ficlog,"Total");
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          }else{
   /* cutv(path,optionfile,pathtot,'\\');*/            if(first==1){
               first=0;
 split(pathtot, path,optionfile);              printf("See log file for details...\n");
   chdir(path);            }
   replace(pathc,path);            fprintf(ficlog,"Age %d", i);
 #endif          }
 #ifdef unix          for(jk=1; jk <=nlstate ; jk++){
   scanf("%s",optionfile);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 #endif              pp[jk] += freq[jk][m][i]; 
           }
 /*-------- arguments in the command line --------*/          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
   strcpy(fileres,"r");              pos += freq[jk][m][i];
   strcat(fileres, optionfile);            if(pp[jk]>=1.e-10){
               if(first==1){
   /*---------arguments file --------*/              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               }
   if((ficpar=fopen(optionfile,"r"))==NULL)    {              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     printf("Problem with optionfile %s\n",optionfile);            }else{
     goto end;              if(first==1)
   }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   strcpy(filereso,"o");            }
   strcat(filereso,fileres);          }
   if((ficparo=fopen(filereso,"w"))==NULL) {  
     printf("Problem with Output resultfile: %s\n", filereso);goto end;          for(jk=1; jk <=nlstate ; jk++){
   }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
   /* Reads comments: lines beginning with '#' */          }       
   while((c=getc(ficpar))=='#' && c!= EOF){          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     ungetc(c,ficpar);            pos += pp[jk];
     fgets(line, MAXLINE, ficpar);            posprop += prop[jk][i];
     puts(line);          }
     fputs(line,ficparo);          for(jk=1; jk <=nlstate ; jk++){
   }            if(pos>=1.e-5){
   ungetc(c,ficpar);              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   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);            }else{
   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);              if(first==1)
 while((c=getc(ficpar))=='#' && c!= EOF){                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     ungetc(c,ficpar);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     fgets(line, MAXLINE, ficpar);            }
     puts(line);            if( i <= iagemax){
     fputs(line,ficparo);              if(pos>=1.e-5){
   }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   ungetc(c,ficpar);                /*probs[i][jk][j1]= pp[jk]/pos;*/
                  /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   fscanf(ficpar,"fprevalence=%s lprevalence=%s pop_based=%d\n",strfprev,strlprev,&popbased);              }
   fprintf(ficparo,"fprevalence=%s lprevalence=%s pop_based=%d\n",strfprev,strlprev,popbased);              else
                  fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   /* printf("%s %s",strfprev,strlprev);            }
      exit(0);*/          }
  while((c=getc(ficpar))=='#' && c!= EOF){          
     ungetc(c,ficpar);          for(jk=-1; jk <=nlstate+ndeath; jk++)
     fgets(line, MAXLINE, ficpar);            for(m=-1; m <=nlstate+ndeath; m++)
     puts(line);              if(freq[jk][m][i] !=0 ) {
     fputs(line,ficparo);              if(first==1)
   }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   ungetc(c,ficpar);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                }
   fscanf(ficpar,"fprevalence=%s lprevalence=%s nforecast=%d mob_average=%d\n",strfprevfore,strlprevfore,&nforecast,&mobilav);          if(i <= iagemax)
   fprintf(ficparo,"fprevalence=%s lprevalence=%s nforecast=%d mob_average=%d\n",strfprevfore,strlprevfore,nforecast,mobilav);            fprintf(ficresp,"\n");
                if(first==1)
              printf("Others in log...\n");
 while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficlog,"\n");
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);      }
     puts(line);    }
     fputs(line,ficparo);    dateintmean=dateintsum/k2cpt; 
   }   
   ungetc(c,ficpar);    fclose(ficresp);
      free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
   fscanf(ficpar,"popforecast=%d popfile=%s\n",&popforecast,popfile);    free_vector(pp,1,nlstate);
      free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   covar=matrix(0,NCOVMAX,1,n);    /* End of Freq */
   cptcovn=0;  }
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  
   /************ Prevalence ********************/
   ncovmodel=2+cptcovn;  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)
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  {  
      /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   /* Read guess parameters */       in each health status at the date of interview (if between dateprev1 and dateprev2).
   /* Reads comments: lines beginning with '#' */       We still use firstpass and lastpass as another selection.
   while((c=getc(ficpar))=='#' && c!= EOF){    */
     ungetc(c,ficpar);   
     fgets(line, MAXLINE, ficpar);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     puts(line);    double ***freq; /* Frequencies */
     fputs(line,ficparo);    double *pp, **prop;
   }    double pos,posprop; 
   ungetc(c,ficpar);    double  y2; /* in fractional years */
      int iagemin, iagemax;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
     for(i=1; i <=nlstate; i++)    iagemin= (int) agemin;
     for(j=1; j <=nlstate+ndeath-1; j++){    iagemax= (int) agemax;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    /*pp=vector(1,nlstate);*/
       fprintf(ficparo,"%1d%1d",i1,j1);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       printf("%1d%1d",i,j);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       for(k=1; k<=ncovmodel;k++){    j1=0;
         fscanf(ficpar," %lf",&param[i][j][k]);    
         printf(" %lf",param[i][j][k]);    j=cptcoveff;
         fprintf(ficparo," %lf",param[i][j][k]);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       }    
       fscanf(ficpar,"\n");    for(k1=1; k1<=j;k1++){
       printf("\n");      for(i1=1; i1<=ncodemax[k1];i1++){
       fprintf(ficparo,"\n");        j1++;
     }        
          for (i=1; i<=nlstate; i++)  
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0.0;
   p=param[1][1];       
          for (i=1; i<=imx; i++) { /* Each individual */
   /* Reads comments: lines beginning with '#' */          bool=1;
   while((c=getc(ficpar))=='#' && c!= EOF){          if  (cptcovn>0) {
     ungetc(c,ficpar);            for (z1=1; z1<=cptcoveff; z1++) 
     fgets(line, MAXLINE, ficpar);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     puts(line);                bool=0;
     fputs(line,ficparo);          } 
   }          if (bool==1) { 
   ungetc(c,ficpar);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   for(i=1; i <=nlstate; i++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     for(j=1; j <=nlstate+ndeath-1; j++){                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); 
       fscanf(ficpar,"%1d%1d",&i1,&j1);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       printf("%1d%1d",i,j);                  /*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(ficparo,"%1d%1d",i1,j1);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       for(k=1; k<=ncovmodel;k++){                  prop[s[m][i]][iagemax+3] += weight[i]; 
         fscanf(ficpar,"%le",&delti3[i][j][k]);                } 
         printf(" %le",delti3[i][j][k]);              }
         fprintf(ficparo," %le",delti3[i][j][k]);            } /* end selection of waves */
       }          }
       fscanf(ficpar,"\n");        }
       printf("\n");        for(i=iagemin; i <= iagemax+3; i++){  
       fprintf(ficparo,"\n");          
     }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   }            posprop += prop[jk][i]; 
   delti=delti3[1][1];          } 
    
   /* Reads comments: lines beginning with '#' */          for(jk=1; jk <=nlstate ; jk++){     
   while((c=getc(ficpar))=='#' && c!= EOF){            if( i <=  iagemax){ 
     ungetc(c,ficpar);              if(posprop>=1.e-5){ 
     fgets(line, MAXLINE, ficpar);                probs[i][jk][j1]= prop[jk][i]/posprop;
     puts(line);              } 
     fputs(line,ficparo);            } 
   }          }/* end jk */ 
   ungetc(c,ficpar);        }/* end i */ 
        } /* end i1 */
   matcov=matrix(1,npar,1,npar);    } /* end k1 */
   for(i=1; i <=npar; i++){    
     fscanf(ficpar,"%s",&str);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     printf("%s",str);    /*free_vector(pp,1,nlstate);*/
     fprintf(ficparo,"%s",str);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     for(j=1; j <=i; j++){  }  /* End of prevalence */
       fscanf(ficpar," %le",&matcov[i][j]);  
       printf(" %.5le",matcov[i][j]);  /************* Waves Concatenation ***************/
       fprintf(ficparo," %.5le",matcov[i][j]);  
     }  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)
     fscanf(ficpar,"\n");  {
     printf("\n");    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     fprintf(ficparo,"\n");       Death is a valid wave (if date is known).
   }       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   for(i=1; i <=npar; i++)       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     for(j=i+1;j<=npar;j++)       and mw[mi+1][i]. dh depends on stepm.
       matcov[i][j]=matcov[j][i];       */
      
   printf("\n");    int i, mi, m;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
     /*-------- data file ----------*/    int first;
     if((ficres =fopen(fileres,"w"))==NULL) {    int j, k=0,jk, ju, jl;
       printf("Problem with resultfile: %s\n", fileres);goto end;    double sum=0.;
     }    first=0;
     fprintf(ficres,"#%s\n",version);    jmin=1e+5;
        jmax=-1;
     if((fic=fopen(datafile,"r"))==NULL)    {    jmean=0.;
       printf("Problem with datafile: %s\n", datafile);goto end;    for(i=1; i<=imx; i++){
     }      mi=0;
       m=firstpass;
     n= lastobs;      while(s[m][i] <= nlstate){
     severity = vector(1,maxwav);        if(s[m][i]>=1)
     outcome=imatrix(1,maxwav+1,1,n);          mw[++mi][i]=m;
     num=ivector(1,n);        if(m >=lastpass)
     moisnais=vector(1,n);          break;
     annais=vector(1,n);        else
     moisdc=vector(1,n);          m++;
     andc=vector(1,n);      }/* end while */
     agedc=vector(1,n);      if (s[m][i] > nlstate){
     cod=ivector(1,n);        mi++;     /* Death is another wave */
     weight=vector(1,n);        /* if(mi==0)  never been interviewed correctly before death */
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */           /* Only death is a correct wave */
     mint=matrix(1,maxwav,1,n);        mw[mi][i]=m;
     anint=matrix(1,maxwav,1,n);      }
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,n);          wav[i]=mi;
     tab=ivector(1,NCOVMAX);      if(mi==0){
     ncodemax=ivector(1,8);        nbwarn++;
         if(first==0){
     i=1;          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     while (fgets(line, MAXLINE, fic) != NULL)    {          first=1;
       if ((i >= firstobs) && (i <=lastobs)) {        }
                if(first==1){
         for (j=maxwav;j>=1;j--){          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        }
           strcpy(line,stra);      } /* end mi==0 */
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    } /* End individuals */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }    for(i=1; i<=imx; i++){
              for(mi=1; mi<wav[i];mi++){
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        if (stepm <=0)
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          dh[mi][i]=1;
         else{
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            if (agedc[i] < 2*AGESUP) {
               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);              if(j==0) j=1;  /* Survives at least one month after exam */
         for (j=ncov;j>=1;j--){              else if(j<0){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                nberr++;
         }                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         num[i]=atol(stra);                j=1; /* Temporary Dangerous patch */
                        printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){                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]);
           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])); ij=ij+1;}*/                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);
               }
         i=i+1;              k=k+1;
       }              if (j >= jmax) jmax=j;
     }              if (j <= jmin) jmin=j;
     /* printf("ii=%d", ij);              sum=sum+j;
        scanf("%d",i);*/              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   imx=i-1; /* Number of individuals */              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
   /* for (i=1; i<=imx; i++){          }
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          else{
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     }            k=k+1;
     for (i=1; i<=imx; i++) 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]));*/            if (j >= jmax) jmax=j;
             else if (j <= jmin)jmin=j;
   /* Calculation of the number of parameter from char model*/            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   Tvar=ivector(1,15);            /*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]);*/
   Tprod=ivector(1,15);            if(j<0){
   Tvaraff=ivector(1,15);              nberr++;
   Tvard=imatrix(1,15,1,2);              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]);
   Tage=ivector(1,15);                    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]);
                }
   if (strlen(model) >1){            sum=sum+j;
     j=0, j1=0, k1=1, k2=1;          }
     j=nbocc(model,'+');          jk= j/stepm;
     j1=nbocc(model,'*');          jl= j -jk*stepm;
     cptcovn=j+1;          ju= j -(jk+1)*stepm;
     cptcovprod=j1;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
                if(jl==0){
                  dh[mi][i]=jk;
     strcpy(modelsav,model);              bh[mi][i]=0;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            }else{ /* We want a negative bias in order to only have interpolation ie
       printf("Error. Non available option model=%s ",model);                    * at the price of an extra matrix product in likelihood */
       goto end;              dh[mi][i]=jk+1;
     }              bh[mi][i]=ju;
                }
     for(i=(j+1); i>=1;i--){          }else{
       cutv(stra,strb,modelsav,'+');            if(jl <= -ju){
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);              dh[mi][i]=jk;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/              bh[mi][i]=jl;       /* bias is positive if real duration
       /*scanf("%d",i);*/                                   * is higher than the multiple of stepm and negative otherwise.
       if (strchr(strb,'*')) {                                   */
         cutv(strd,strc,strb,'*');            }
         if (strcmp(strc,"age")==0) {            else{
           cptcovprod--;              dh[mi][i]=jk+1;
           cutv(strb,stre,strd,'V');              bh[mi][i]=ju;
           Tvar[i]=atoi(stre);            }
           cptcovage++;            if(dh[mi][i]==0){
             Tage[cptcovage]=i;              dh[mi][i]=1; /* At least one step */
             /*printf("stre=%s ", stre);*/              bh[mi][i]=ju; /* At least one step */
         }              /*  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);*/
         else if (strcmp(strd,"age")==0) {            }
           cptcovprod--;          } /* end if mle */
           cutv(strb,stre,strc,'V');        }
           Tvar[i]=atoi(stre);      } /* end wave */
           cptcovage++;    }
           Tage[cptcovage]=i;    jmean=sum/k;
         }    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
         else {    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           cutv(strb,stre,strc,'V');   }
           Tvar[i]=ncov+k1;  
           cutv(strb,strc,strd,'V');  /*********** Tricode ****************************/
           Tprod[k1]=i;  void tricode(int *Tvar, int **nbcode, int imx)
           Tvard[k1][1]=atoi(strc);  {
           Tvard[k1][2]=atoi(stre);    
           Tvar[cptcovn+k2]=Tvard[k1][1];    int Ndum[20],ij=1, k, j, i, maxncov=19;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    int cptcode=0;
           for (k=1; k<=lastobs;k++)    cptcoveff=0; 
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];   
           k1++;    for (k=0; k<maxncov; k++) Ndum[k]=0;
           k2=k2+2;    for (k=1; k<=7; k++) ncodemax[k]=0;
         }  
       }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       else {      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/                                 modality*/ 
        /*  scanf("%d",i);*/        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
       cutv(strd,strc,strb,'V');        Ndum[ij]++; /*store the modality */
       Tvar[i]=atoi(strc);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       }        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
       strcpy(modelsav,stra);                                           Tvar[j]. If V=sex and male is 0 and 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                                         female is 1, then  cptcode=1.*/
         scanf("%d",i);*/      }
     }  
 }      for (i=0; i<=cptcode; i++) {
          if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      }
   printf("cptcovprod=%d ", cptcovprod);  
   scanf("%d ",i);*/      ij=1; 
     fclose(fic);      for (i=1; i<=ncodemax[j]; i++) {
         for (k=0; k<= maxncov; k++) {
     /*  if(mle==1){*/          if (Ndum[k] != 0) {
     if (weightopt != 1) { /* Maximisation without weights*/            nbcode[Tvar[j]][ij]=k; 
       for(i=1;i<=n;i++) weight[i]=1.0;            /* 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; */
     }            
     /*-calculation of age at interview from date of interview and age at death -*/            ij++;
     agev=matrix(1,maxwav,1,imx);          }
           if (ij > ncodemax[j]) break; 
    for (i=1; i<=imx; i++)        }  
      for(m=2; (m<= maxwav); m++)      } 
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    }  
          anint[m][i]=9999;  
          s[m][i]=-1;   for (k=0; k< maxncov; k++) Ndum[k]=0;
        }  
       for (i=1; i<=ncovmodel-2; i++) { 
     for (i=1; i<=imx; i++)  {     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);     ij=Tvar[i];
       for(m=1; (m<= maxwav); m++){     Ndum[ij]++;
         if(s[m][i] >0){   }
           if (s[m][i] == nlstate+1) {  
             if(agedc[i]>0)   ij=1;
               if(moisdc[i]!=99 && andc[i]!=9999)   for (i=1; i<= maxncov; i++) {
               agev[m][i]=agedc[i];     if((Ndum[i]!=0) && (i<=ncovcol)){
             else {       Tvaraff[ij]=i; /*For printing */
               if (andc[i]!=9999){       ij++;
               printf("Warning negative age at death: %d line:%d\n",num[i],i);     }
               agev[m][i]=-1;   }
               }   
             }   cptcoveff=ij-1; /*Number of simple covariates*/
           }  }
           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]);  /*********** Health Expectancies ****************/
             if(mint[m][i]==99 || anint[m][i]==9999)  
               agev[m][i]=1;  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 )
             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);*/    /* Health expectancies */
             }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
             else if(agev[m][i] >agemax){    double age, agelim, hf;
               agemax=agev[m][i];    double ***p3mat,***varhe;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    double **dnewm,**doldm;
             }    double *xp;
             /*agev[m][i]=anint[m][i]-annais[i];*/    double **gp, **gm;
             /*   agev[m][i] = age[i]+2*m;*/    double ***gradg, ***trgradg;
           }    int theta;
           else { /* =9 */  
             agev[m][i]=1;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
             s[m][i]=-1;    xp=vector(1,npar);
           }    dnewm=matrix(1,nlstate*nlstate,1,npar);
         }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
         else /*= 0 Unknown */    
           agev[m][i]=1;    fprintf(ficreseij,"# Health expectancies\n");
       }    fprintf(ficreseij,"# Age");
        for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=nlstate;j++)
     for (i=1; i<=imx; i++)  {        fprintf(ficreseij," %1d-%1d (SE)",i,j);
       for(m=1; (m<= maxwav); m++){    fprintf(ficreseij,"\n");
         if (s[m][i] > (nlstate+ndeath)) {  
           printf("Error: Wrong value in nlstate or ndeath\n");      if(estepm < stepm){
           goto end;      printf ("Problem %d lower than %d\n",estepm, stepm);
         }    }
       }    else  hstepm=estepm;   
     }    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);     * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
     free_vector(severity,1,maxwav);     * progression in between and thus overestimating or underestimating according
     free_imatrix(outcome,1,maxwav+1,1,n);     * to the curvature of the survival function. If, for the same date, we 
     free_vector(moisnais,1,n);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     free_vector(annais,1,n);     * to compare the new estimate of Life expectancy with the same linear 
     /* free_matrix(mint,1,maxwav,1,n);     * hypothesis. A more precise result, taking into account a more precise
        free_matrix(anint,1,maxwav,1,n);*/     * curvature will be obtained if estepm is as small as stepm. */
     free_vector(moisdc,1,n);  
     free_vector(andc,1,n);    /* 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 
     wav=ivector(1,imx);       nstepm is the number of stepm from age to agelin. 
     dh=imatrix(1,lastpass-firstpass+1,1,imx);       Look at hpijx to understand the reason of that which relies in memory size
     mw=imatrix(1,lastpass-firstpass+1,1,imx);       and note for a fixed period like estepm months */
        /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     /* Concatenates waves */       survival function given by stepm (the optimization length). Unfortunately it
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);       means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
       Tcode=ivector(1,100);    */
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       ncodemax[1]=1;  
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    agelim=AGESUP;
          for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
    codtab=imatrix(1,100,1,10);      /* nhstepm age range expressed in number of stepm */
    h=0;      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
    m=pow(2,cptcoveff);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        /* if (stepm >= YEARM) hstepm=1;*/
    for(k=1;k<=cptcoveff; k++){      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
      for(i=1; i <=(m/pow(2,k));i++){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        for(j=1; j <= ncodemax[k]; j++){      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      gp=matrix(0,nhstepm,1,nlstate*nlstate);
            h++;      gm=matrix(0,nhstepm,1,nlstate*nlstate);
            if (h>m) h=1;codtab[h][k]=j;  
          }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
        }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
      }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
    }   
      
    /* Calculates basic frequencies. Computes observed prevalence at single age      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        and prints on file fileres'p'. */  
       /* Computing  Variances of health expectancies */
     if ((nbocc(strfprev,'/')==1) && (nbocc(strlprev,'/')==1)){  
      boolprev=0;       for(theta=1; theta <=npar; theta++){
      cutv(stra,strb,strfprev,'/');        for(i=1; i<=npar; i++){ 
      dateprev1=(double)(atoi(strb)+atoi(stra)/12.);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
      cutv(stra,strb,strlprev,'/');        }
      dateprev2=(double)(atoi(strb)+atoi(stra)/12.);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
    }    
            cptj=0;
    else if ((nbocc(strfprev,'/')==0) &&(nbocc(strlprev,'/')==0)){        for(j=1; j<= nlstate; j++){
      boolprev=1;          for(i=1; i<=nlstate; i++){
      fprev=atoi(strfprev); lprev=atoi(strlprev);            cptj=cptj+1;
    }            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
     else {              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       printf("Error in statement lprevalence or fprevalence\n");            }
       goto end;          }
     }        }
           
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev,mint,anint,boolprev,dateprev1,dateprev2);       
          for(i=1; i<=npar; i++) 
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        cptj=0;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        for(j=1; j<= nlstate; j++){
                for(i=1;i<=nlstate;i++){
     /* For Powell, parameters are in a vector p[] starting at p[1]            cptj=cptj+1;
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  
               gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     if(mle==1){            }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          }
     }        }
            for(j=1; j<= nlstate*nlstate; j++)
     /*--------- results files --------------*/          for(h=0; h<=nhstepm-1; h++){
     fprintf(ficres,"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);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
    fprintf(ficres,"fprevalence=%s lprevalence=%s pop_based=%d\n",strfprev,strlprev,popbased);          }
    fprintf(ficres,"fprevalence=%s lprevalence=%s nforecast=%d mob_average=%d\n",strfprevfore,strlprevfore,nforecast,mobilav);       } 
      
    jk=1;  /* End theta */
    fprintf(ficres,"# Parameters\n");  
    printf("# Parameters\n");       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
    for(i=1,jk=1; i <=nlstate; i++){  
      for(k=1; k <=(nlstate+ndeath); k++){       for(h=0; h<=nhstepm-1; h++)
        if (k != i)        for(j=1; j<=nlstate*nlstate;j++)
          {          for(theta=1; theta <=npar; theta++)
            printf("%d%d ",i,k);            trgradg[h][j][theta]=gradg[h][theta][j];
            fprintf(ficres,"%1d%1d ",i,k);       
            for(j=1; j <=ncovmodel; j++){  
              printf("%f ",p[jk]);       for(i=1;i<=nlstate*nlstate;i++)
              fprintf(ficres,"%f ",p[jk]);        for(j=1;j<=nlstate*nlstate;j++)
              jk++;          varhe[i][j][(int)age] =0.;
            }  
            printf("\n");       printf("%d|",(int)age);fflush(stdout);
            fprintf(ficres,"\n");       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
          }       for(h=0;h<=nhstepm-1;h++){
      }        for(k=0;k<=nhstepm-1;k++){
    }          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
  if(mle==1){          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     /* Computing hessian and covariance matrix */          for(i=1;i<=nlstate*nlstate;i++)
     ftolhess=ftol; /* Usually correct */            for(j=1;j<=nlstate*nlstate;j++)
     hesscov(matcov, p, npar, delti, ftolhess, func);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
  }        }
     fprintf(ficres,"# Scales\n");      }
     printf("# Scales\n");      /* Computing expectancies */
      for(i=1,jk=1; i <=nlstate; i++){      for(i=1; i<=nlstate;i++)
       for(j=1; j <=nlstate+ndeath; j++){        for(j=1; j<=nlstate;j++)
         if (j!=i) {          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           fprintf(ficres,"%1d%1d",i,j);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
           printf("%1d%1d",i,j);            
           for(k=1; k<=ncovmodel;k++){  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
             printf(" %.5e",delti[jk]);  
             fprintf(ficres," %.5e",delti[jk]);          }
             jk++;  
           }      fprintf(ficreseij,"%3.0f",age );
           printf("\n");      cptj=0;
           fprintf(ficres,"\n");      for(i=1; i<=nlstate;i++)
         }        for(j=1; j<=nlstate;j++){
       }          cptj++;
      }          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
            }
     k=1;      fprintf(ficreseij,"\n");
     fprintf(ficres,"# Covariance\n");     
     printf("# Covariance\n");      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     for(i=1;i<=npar;i++){      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       /*  if (k>nlstate) k=1;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
       i1=(i-1)/(ncovmodel*nlstate)+1;      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       printf("%s%d%d",alph[k],i1,tab[i]);*/    }
       fprintf(ficres,"%3d",i);    printf("\n");
       printf("%3d",i);    fprintf(ficlog,"\n");
       for(j=1; j<=i;j++){  
         fprintf(ficres," %.5e",matcov[i][j]);    free_vector(xp,1,npar);
         printf(" %.5e",matcov[i][j]);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
       }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       fprintf(ficres,"\n");    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
       printf("\n");  }
       k++;  
     }  /************ Variance ******************/
      void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
     while((c=getc(ficpar))=='#' && c!= EOF){  {
       ungetc(c,ficpar);    /* Variance of health expectancies */
       fgets(line, MAXLINE, ficpar);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       puts(line);    /* double **newm;*/
       fputs(line,ficparo);    double **dnewm,**doldm;
     }    double **dnewmp,**doldmp;
     ungetc(c,ficpar);    int i, j, nhstepm, hstepm, h, nstepm ;
      int k, cptcode;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    double *xp;
        double **gp, **gm;  /* for var eij */
     if (fage <= 2) {    double ***gradg, ***trgradg; /*for var eij */
       bage = agemin;    double **gradgp, **trgradgp; /* for var p point j */
       fage = agemax;    double *gpp, *gmp; /* for var p point j */
     }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    double age,agelim, hf;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    double ***mobaverage;
     int theta;
        char digit[4];
 /*------------ gnuplot -------------*/    char digitp[25];
 chdir(pathcd);  
   if((ficgp=fopen("graph.plt","w"))==NULL) {    char fileresprobmorprev[FILENAMELENGTH];
     printf("Problem with file graph.gp");goto end;  
   }    if(popbased==1){
 #ifdef windows      if(mobilav!=0)
   fprintf(ficgp,"cd \"%s\" \n",pathc);        strcpy(digitp,"-populbased-mobilav-");
 #endif      else strcpy(digitp,"-populbased-nomobil-");
 m=pow(2,cptcoveff);    }
      else 
  /* 1eme*/      strcpy(digitp,"-stablbased-");
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {    if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 #ifdef windows      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=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);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
 #endif        printf(" Error in movingaverage mobilav=%d\n",mobilav);
 #ifdef unix      }
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    }
 #endif  
     strcpy(fileresprobmorprev,"prmorprev"); 
 for (i=1; i<= nlstate ; i ++) {    sprintf(digit,"%-d",ij);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");    strcat(fileresprobmorprev,digit); /* Tvar to be done */
 }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    strcat(fileresprobmorprev,fileres);
     for (i=1; i<= nlstate ; i ++) {    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
 }    }
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      for (i=1; i<= nlstate ; i ++) {    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
 }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      fprintf(ficresprobmorprev," p.%-d SE",j);
 #ifdef unix      for(i=1; i<=nlstate;i++)
 fprintf(ficgp,"\nset ter gif small size 400,300");        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
 #endif    }  
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    fprintf(ficresprobmorprev,"\n");
    }    fprintf(ficgp,"\n# Routine varevsij");
   }    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");
   /*2 eme*/    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
   for (k1=1; k1<= m ; k1 ++) {    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);  
        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");
     for (i=1; i<= nlstate+1 ; i ++) {    fprintf(ficresvij,"# Age");
       k=2*i;    for(i=1; i<=nlstate;i++)
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      for(j=1; j<=nlstate;j++)
       for (j=1; j<= nlstate+1 ; j ++) {        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficresvij,"\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      xp=vector(1,npar);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    dnewm=matrix(1,nlstate,1,npar);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    doldm=matrix(1,nlstate,1,nlstate);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
       for (j=1; j<= nlstate+1 ; j ++) {    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
         else fprintf(ficgp," \%%*lf (\%%*lf)");    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
 }      gpp=vector(nlstate+1,nlstate+ndeath);
       fprintf(ficgp,"\" t\"\" w l 0,");    gmp=vector(nlstate+1,nlstate+ndeath);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       for (j=1; j<= nlstate+1 ; j ++) {    
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    if(estepm < stepm){
   else fprintf(ficgp," \%%*lf (\%%*lf)");      printf ("Problem %d lower than %d\n",estepm, stepm);
 }      }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    else  hstepm=estepm;   
       else fprintf(ficgp,"\" t\"\" w l 0,");    /* 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. 
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);       nhstepm is the number of hstepm from age to agelim 
   }       nstepm is the number of stepm from age to agelin. 
         Look at hpijx to understand the reason of that which relies in memory size
   /*3eme*/       and note for a fixed period like k years */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   for (k1=1; k1<= m ; k1 ++) {       survival function given by stepm (the optimization length). Unfortunately it
     for (cpt=1; cpt<= nlstate ; cpt ++) {       means that if the survival funtion is printed every two years of age and if
       k=2+nlstate*(cpt-1);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       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);       results. So we changed our mind and took the option of the best precision.
       for (i=1; i< nlstate ; i ++) {    */
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       }    agelim = AGESUP;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     }      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /* CV preval stat */      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   for (k1=1; k1<= m ; k1 ++) {      gp=matrix(0,nhstepm,1,nlstate);
     for (cpt=1; cpt<nlstate ; cpt ++) {      gm=matrix(0,nhstepm,1,nlstate);
       k=3;  
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);  
       for (i=1; i< nlstate ; i ++)      for(theta=1; theta <=npar; theta++){
         fprintf(ficgp,"+$%d",k+i+1);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
              }
       l=3+(nlstate+ndeath)*cpt;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       for (i=1; i< nlstate ; i ++) {  
         l=3+(nlstate+ndeath)*cpt;        if (popbased==1) {
         fprintf(ficgp,"+$%d",l+i+1);          if(mobilav ==0){
       }            for(i=1; i<=nlstate;i++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                prlim[i][i]=probs[(int)age][i][ij];
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          }else{ /* mobilav */ 
     }            for(i=1; i<=nlstate;i++)
   }                prlim[i][i]=mobaverage[(int)age][i][ij];
           }
   /* proba elementaires */        }
    for(i=1,jk=1; i <=nlstate; i++){    
     for(k=1; k <=(nlstate+ndeath); k++){        for(j=1; j<= nlstate; j++){
       if (k != i) {          for(h=0; h<=nhstepm; h++){
         for(j=1; j <=ncovmodel; j++){            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           /*fprintf(ficgp,"%s",alph[1]);*/          }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        }
           jk++;        /* This for computing probability of death (h=1 means
           fprintf(ficgp,"\n");           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];
   for(jk=1; jk <=m; jk++) {        }    
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);        /* end probability of death */
    i=1;  
    for(k2=1; k2<=nlstate; k2++) {        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
      k3=i;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
      for(k=1; k<=(nlstate+ndeath); k++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        if (k != k2){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);   
 ij=1;        if (popbased==1) {
         for(j=3; j <=ncovmodel; j++) {          if(mobilav ==0){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {            for(i=1; i<=nlstate;i++)
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);              prlim[i][i]=probs[(int)age][i][ij];
             ij++;          }else{ /* mobilav */ 
           }            for(i=1; i<=nlstate;i++)
           else              prlim[i][i]=mobaverage[(int)age][i][ij];
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          }
         }        }
           fprintf(ficgp,")/(1");  
                for(j=1; j<= nlstate; j++){
         for(k1=1; k1 <=nlstate; k1++){            for(h=0; h<=nhstepm; h++){
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
 ij=1;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           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]]]);        /* This for computing probability of death (h=1 means
             ij++;           computed over hstepm matrices product = hstepm*stepm months) 
           }           as a weighted average of prlim.
           else        */
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
           fprintf(ficgp,")");           gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }        }    
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        /* end probability of death */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");  
         i=i+ncovmodel;        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];
    }          }
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  
   }        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
              gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   fclose(ficgp);        }
      
 chdir(path);      } /* End theta */
      
     free_ivector(wav,1,imx);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        for(h=0; h<=nhstepm; h++) /* veij */
     free_ivector(num,1,n);        for(j=1; j<=nlstate;j++)
     free_vector(agedc,1,n);          for(theta=1; theta <=npar; theta++)
     /*free_matrix(covar,1,NCOVMAX,1,n);*/            trgradg[h][j][theta]=gradg[h][theta][j];
     fclose(ficparo);  
     fclose(ficres);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     /*  }*/        for(theta=1; theta <=npar; theta++)
              trgradgp[j][theta]=gradgp[theta][j];
    /*________fin mle=1_________*/    
      
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        for(i=1;i<=nlstate;i++)
     /* No more information from the sample is required now */        for(j=1;j<=nlstate;j++)
   /* Reads comments: lines beginning with '#' */          vareij[i][j][(int)age] =0.;
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      for(h=0;h<=nhstepm;h++){
     fgets(line, MAXLINE, ficpar);        for(k=0;k<=nhstepm;k++){
     puts(line);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     fputs(line,ficparo);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   }          for(i=1;i<=nlstate;i++)
   ungetc(c,ficpar);            for(j=1;j<=nlstate;j++)
                vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);        }
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);      }
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    
 /*--------- index.htm --------*/      /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   strcpy(optionfilehtm,optionfile);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   strcat(optionfilehtm,".htm");      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     printf("Problem with %s \n",optionfilehtm);goto end;          varppt[j][i]=doldmp[j][i];
   }      /* end ppptj */
       /*  x centered again */
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
 Total number of observations=%d <br>   
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>      if (popbased==1) {
 <hr  size=\"2\" color=\"#EC5E5E\">        if(mobilav ==0){
 <li>Outputs files<br><br>\n          for(i=1; i<=nlstate;i++)
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n            prlim[i][i]=probs[(int)age][i][ij];
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>        }else{ /* mobilav */ 
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>          for(i=1; i<=nlstate;i++)
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>            prlim[i][i]=mobaverage[(int)age][i][ij];
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>        }
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>      }
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>               
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>      /* This for computing probability of death (h=1 means
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>         as a weighted average of prlim.
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);      */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
  fprintf(fichtm," <li>Graphs</li><p>");        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
  m=cptcoveff;      }    
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      /* end probability of death */
   
  j1=0;      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
  for(k1=1; k1<=m;k1++){      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
    for(i1=1; i1<=ncodemax[k1];i1++){        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
        j1++;        for(i=1; i<=nlstate;i++){
        if (cptcovn > 0) {          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
          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[j1][cpt]]);      fprintf(ficresprobmorprev,"\n");
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  
        }      fprintf(ficresvij,"%.0f ",age );
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      for(i=1; i<=nlstate;i++)
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            for(j=1; j<=nlstate;j++){
        for(cpt=1; cpt<nlstate;cpt++){          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>        }
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      fprintf(ficresvij,"\n");
        }      free_matrix(gp,0,nhstepm,1,nlstate);
     for(cpt=1; cpt<=nlstate;cpt++) {      free_matrix(gm,0,nhstepm,1,nlstate);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
 interval) in state (%d): v%s%d%d.gif <br>      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      }    } /* End age */
      for(cpt=1; cpt<=nlstate;cpt++) {    free_vector(gpp,nlstate+1,nlstate+ndeath);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    free_vector(gmp,nlstate+1,nlstate+ndeath);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
      }    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
 health expectancies in states (1) and (2): e%s%d.gif<br>    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
 fprintf(fichtm,"\n</body>");  /*   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); */
 fclose(fichtm);    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));
   /*--------------- Prevalence limit --------------*/    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));
   strcpy(filerespl,"pl");    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);
   strcat(filerespl,fileres);    /*  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);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  /*   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);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  
   fprintf(ficrespl,"#Prevalence limit\n");    free_vector(xp,1,npar);
   fprintf(ficrespl,"#Age ");    free_matrix(doldm,1,nlstate,1,nlstate);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    free_matrix(dnewm,1,nlstate,1,npar);
   fprintf(ficrespl,"\n");    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   prlim=matrix(1,nlstate,1,nlstate);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fclose(ficresprobmorprev);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fflush(ficgp);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fflush(fichtm); 
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  }  /* end varevsij */
   k=0;  
   agebase=agemin;  /************ Variance of prevlim ******************/
   agelim=agemax;  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)
   ftolpl=1.e-10;  {
   i1=cptcoveff;    /* Variance of prevalence limit */
   if (cptcovn < 1){i1=1;}    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
   for(cptcov=1;cptcov<=i1;cptcov++){    double **dnewm,**doldm;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int i, j, nhstepm, hstepm;
         k=k+1;    int k, cptcode;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    double *xp;
         fprintf(ficrespl,"\n#******");    double *gp, *gm;
         for(j=1;j<=cptcoveff;j++)    double **gradg, **trgradg;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double age,agelim;
         fprintf(ficrespl,"******\n");    int theta;
             
         for (age=agebase; age<=agelim; age++){    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    fprintf(ficresvpl,"# Age");
           fprintf(ficrespl,"%.0f",age );    for(i=1; i<=nlstate;i++)
           for(i=1; i<=nlstate;i++)        fprintf(ficresvpl," %1d-%1d",i,i);
           fprintf(ficrespl," %.5f", prlim[i][i]);    fprintf(ficresvpl,"\n");
           fprintf(ficrespl,"\n");  
         }    xp=vector(1,npar);
       }    dnewm=matrix(1,nlstate,1,npar);
     }    doldm=matrix(1,nlstate,1,nlstate);
   fclose(ficrespl);    
     hstepm=1*YEARM; /* Every year of age */
   /*------------- h Pij x at various ages ------------*/    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
      agelim = AGESUP;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      if (stepm >= YEARM) hstepm=1;
   }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   printf("Computing pij: result on file '%s' \n", filerespij);      gradg=matrix(1,npar,1,nlstate);
        gp=vector(1,nlstate);
   stepsize=(int) (stepm+YEARM-1)/YEARM;      gm=vector(1,nlstate);
   /*if (stepm<=24) stepsize=2;*/  
       for(theta=1; theta <=npar; theta++){
   agelim=AGESUP;        for(i=1; i<=npar; i++){ /* Computes gradient */
   hstepm=stepsize*YEARM; /* Every year of age */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */        }
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   k=0;        for(i=1;i<=nlstate;i++)
   for(cptcov=1;cptcov<=i1;cptcov++){          gp[i] = prlim[i][i];
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      
       k=k+1;        for(i=1; i<=npar; i++) /* Computes gradient */
         fprintf(ficrespij,"\n#****** ");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         for(j=1;j<=cptcoveff;j++)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(i=1;i<=nlstate;i++)
         fprintf(ficrespij,"******\n");          gm[i] = prlim[i][i];
          
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        for(i=1;i<=nlstate;i++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      } /* End theta */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;      trgradg =matrix(1,nlstate,1,npar);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");      for(j=1; j<=nlstate;j++)
           for(i=1; i<=nlstate;i++)        for(theta=1; theta <=npar; theta++)
             for(j=1; j<=nlstate+ndeath;j++)          trgradg[j][theta]=gradg[theta][j];
               fprintf(ficrespij," %1d-%1d",i,j);  
           fprintf(ficrespij,"\n");      for(i=1;i<=nlstate;i++)
           for (h=0; h<=nhstepm; h++){        varpl[i][(int)age] =0.;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
             for(i=1; i<=nlstate;i++)      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
               for(j=1; j<=nlstate+ndeath;j++)      for(i=1;i<=nlstate;i++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
             fprintf(ficrespij,"\n");  
           }      fprintf(ficresvpl,"%.0f ",age );
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(i=1; i<=nlstate;i++)
           fprintf(ficrespij,"\n");        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);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/      free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   fclose(ficrespij);  
     free_vector(xp,1,npar);
   /*---------- Forecasting ------------------*/    free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   strcpy(fileresf,"f");  
   strcat(fileresf,fileres);  }
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;  /************ 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)
   printf("Computing forecasting: result on file '%s' \n", fileresf);  {
     int i, j=0,  i1, k1, l1, t, tj;
  if ((nbocc(strfprevfore,'/')==1) && (nbocc(strlprevfore,'/')==1)){    int k2, l2, j1,  z1;
      boolprev=0;    int k=0,l, cptcode;
      cutv(stra,strb,strfprevfore,'/');    int first=1, first1;
      dateprev1=(double)(atoi(strb)+atoi(stra)/12.);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
      cutv(stra,strb,strlprevfore,'/');    double **dnewm,**doldm;
      dateprev2=(double)(atoi(strb)+atoi(stra)/12.);    double *xp;
    }    double *gp, *gm;
        double **gradg, **trgradg;
    else if ((nbocc(strfprevfore,'/')==0) &&(nbocc(strlprevfore,'/')==0)){    double **mu;
      boolprev=1;    double age,agelim, cov[NCOVMAX];
      fprev=atoi(strfprevfore); lprev=atoi(strlprevfore);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
    }    int theta;
     else {    char fileresprob[FILENAMELENGTH];
       printf("Error in statement lprevalence or fprevalence\n");    char fileresprobcov[FILENAMELENGTH];
       goto end;    char fileresprobcor[FILENAMELENGTH];
     }  
     double ***varpij;
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprevfore, lprevfore,mint,anint,boolprev,dateprev1,dateprev2);  
      strcpy(fileresprob,"prob"); 
   free_matrix(mint,1,maxwav,1,n);    strcat(fileresprob,fileres);
   free_matrix(anint,1,maxwav,1,n);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   free_matrix(agev,1,maxwav,1,imx);      printf("Problem with resultfile: %s\n", fileresprob);
   /* Mobile average */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
   if (mobilav==1) {    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      printf("Problem with resultfile: %s\n", fileresprobcov);
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       for (i=1; i<=nlstate;i++)    }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    strcpy(fileresprobcor,"probcor"); 
           mobaverage[(int)agedeb][i][cptcod]=0.;    strcat(fileresprobcor,fileres);
        if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     for (agedeb=bage+4; agedeb<=fage; agedeb++){      printf("Problem with resultfile: %s\n", fileresprobcor);
       for (i=1; i<=nlstate;i++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    }
           for (cpt=0;cpt<=4;cpt++){    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    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);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    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");
   stepsize=(int) (stepm+YEARM-1)/YEARM;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   if (stepm<=12) stepsize=1;    fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   agelim=AGESUP;    fprintf(ficresprobcov,"# Age");
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */  
      for(i=1; i<=nlstate;i++)
   if (popforecast==1) {      for(j=1; j<=(nlstate+ndeath);j++){
     if((ficpop=fopen(popfile,"r"))==NULL)    {        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
       printf("Problem with population file : %s\n",popfile);goto end;        fprintf(ficresprobcov," p%1d-%1d ",i,j);
     }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     popage=ivector(0,AGESUP);      }  
     popeffectif=vector(0,AGESUP);   /* fprintf(ficresprob,"\n");
     popcount=vector(0,AGESUP);    fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
     i=1;     */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)   xp=vector(1,npar);
       {    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         i=i+1;    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       }    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     imx=i;    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
      first=1;
   for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    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");
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
       k=k+1;    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
       fprintf(ficresf,"\n#****** ");    file %s<br>\n",optionfilehtmcov);
       for(j=1;j<=cptcoveff;j++) {    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
         fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  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(ficresf,"******\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. \
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
       if (popforecast==1)  fprintf(ficresf," [Population]");  standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
       for (agedeb=fage; agedeb>=bage; agedeb--){   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
         fprintf(ficresf,"\n%.f %.f 0",agedeb, agedeb);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
        if (mobilav==1) {  
         for(j=1; j<=nlstate;j++)    cov[1]=1;
           fprintf(ficresf," %.3f",mobaverage[(int)agedeb][j][cptcod]);    tj=cptcoveff;
         }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
         else {    j1=0;
           for(j=1; j<=nlstate;j++)    for(t=1; t<=tj;t++){
           fprintf(ficresf," %.3f",probs[(int)agedeb][j][cptcod]);      for(i1=1; i1<=ncodemax[t];i1++){ 
         }          j1++;
         if  (cptcovn>0) {
        for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");          fprintf(ficresprob, "\n#********** Variable "); 
        if (popforecast==1) fprintf(ficresf," [%.f] ",popeffectif[(int)agedeb]);          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 (cpt=1; cpt<=nforecast;cpt++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficresf,"\n");          fprintf(ficresprobcov, "**********\n#\n");
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          fprintf(ficgp, "\n#********** Variable "); 
         nhstepm = nhstepm/hstepm;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/          fprintf(ficgp, "**********\n#\n");
           
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          
         oldm=oldms;savm=savms;          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            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\">");
         for (h=0; h<=nhstepm; h++){          
                  fprintf(ficresprobcor, "\n#********** Variable ");    
          if (h*hstepm/YEARM*stepm==cpt)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             fprintf(ficresf,"\n%.f %.f %.f",agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);          fprintf(ficresprobcor, "**********\n#");    
                  }
                  
          for(j=1; j<=nlstate+ndeath;j++) {        for (age=bage; age<=fage; age ++){ 
            kk1=0.;kk2=0;          cov[2]=age;
            for(i=1; i<=nlstate;i++) {                  for (k=1; k<=cptcovn;k++) {
              if (mobilav==1)            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];          }
              else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
              if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];          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 (h*hstepm/YEARM*stepm==cpt) {          
              fprintf(ficresf," %.3f", kk1);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
                if (popforecast==1) fprintf(ficresf," [%.f]", kk2);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
            }          gp=vector(1,(nlstate)*(nlstate+ndeath));
           }          gm=vector(1,(nlstate)*(nlstate+ndeath));
         }      
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          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);
   }            
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            k=0;
   if (popforecast==1) {            for(i=1; i<= (nlstate); i++){
     free_ivector(popage,0,AGESUP);              for(j=1; j<=(nlstate+ndeath);j++){
     free_vector(popeffectif,0,AGESUP);                k=k+1;
     free_vector(popcount,0,AGESUP);                gp[k]=pmmij[i][j];
   }              }
   free_imatrix(s,1,maxwav+1,1,n);            }
   free_vector(weight,1,n);            
   fclose(ficresf);            for(i=1; i<=npar; i++)
   /*---------- Health expectancies and variances ------------*/              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
   strcpy(filerest,"t");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   strcat(filerest,fileres);            k=0;
   if((ficrest=fopen(filerest,"w"))==NULL) {            for(i=1; i<=(nlstate); i++){
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;              for(j=1; j<=(nlstate+ndeath);j++){
   }                k=k+1;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                gm[k]=pmmij[i][j];
               }
             }
   strcpy(filerese,"e");       
   strcat(filerese,fileres);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   if((ficreseij=fopen(filerese,"w"))==NULL) {              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          }
   }  
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
  strcpy(fileresv,"v");              trgradg[j][theta]=gradg[theta][j];
   strcat(fileresv,fileres);          
   if((ficresvij=fopen(fileresv,"w"))==NULL) {          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   }          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   k=0;          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          pmij(pmmij,cov,ncovmodel,x,nlstate);
       k=k+1;          
       fprintf(ficrest,"\n#****** ");          k=0;
       for(j=1;j<=cptcoveff;j++)          for(i=1; i<=(nlstate); i++){
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for(j=1; j<=(nlstate+ndeath);j++){
       fprintf(ficrest,"******\n");              k=k+1;
               mu[k][(int) age]=pmmij[i][j];
       fprintf(ficreseij,"\n#****** ");            }
       for(j=1;j<=cptcoveff;j++)          }
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
       fprintf(ficreseij,"******\n");            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
       fprintf(ficresvij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)          /*printf("\n%d ",(int)age);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       fprintf(ficresvij,"******\n");            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]));
       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);            fprintf(ficresprob,"\n%d ",(int)age);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          fprintf(ficresprobcov,"\n%d ",(int)age);
       oldm=oldms;savm=savms;          fprintf(ficresprobcor,"\n%d ",(int)age);
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
                for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       fprintf(ficrest,"\n");            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                    fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
       hf=1;          }
       if (stepm >= YEARM) hf=stepm/YEARM;          i=0;
       epj=vector(1,nlstate+1);          for (k=1; k<=(nlstate);k++){
       for(age=bage; age <=fage ;age++){            for (l=1; l<=(nlstate+ndeath);l++){ 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);              i=i++;
         if (popbased==1) {              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
           for(i=1; i<=nlstate;i++)              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
             prlim[i][i]=probs[(int)age][i][k];              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]));
         fprintf(ficrest," %.0f",age);              }
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){            }
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          }/* end of loop for state */
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];        } /* end of loop for age */
           }  
           epj[nlstate+1] +=epj[j];        /* Confidence intervalle of pij  */
         }        /*
         for(i=1, vepp=0.;i <=nlstate;i++)          fprintf(ficgp,"\nset noparametric;unset label");
           for(j=1;j <=nlstate;j++)          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
             vepp += vareij[i][j][(int)age];          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));          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);
         for(j=1;j <=nlstate;j++){          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
         }          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         fprintf(ficrest,"\n");        */
       }  
     }        /* 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;
  fclose(ficreseij);            for (k1=1; k1<=(nlstate);k1++){
  fclose(ficresvij);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   fclose(ficrest);                if(l1==k1) continue;
   fclose(ficpar);                i=(k1-1)*(nlstate+ndeath)+l1;
   free_vector(epj,1,nlstate+1);                if(i<=j) continue;
   /*  scanf("%d ",i); */                for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
   /*------- Variance limit prevalence------*/                      v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
 strcpy(fileresvpl,"vpl");                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   strcat(fileresvpl,fileres);                    mu1=mu[i][(int) age]/stepm*YEARM ;
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {                    mu2=mu[j][(int) age]/stepm*YEARM;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);                    c12=cv12/sqrt(v1*v2);
     exit(0);                    /* Computing eigen value of matrix of covariance */
   }                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
  k=0;                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
  for(cptcov=1;cptcov<=i1;cptcov++){                    /*v21=sqrt(1.-v11*v11); *//* error */
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    v21=(lc1-v1)/cv12*v11;
      k=k+1;                    v12=-v21;
      fprintf(ficresvpl,"\n#****** ");                    v22=v11;
      for(j=1;j<=cptcoveff;j++)                    tnalp=v21/v11;
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    if(first1==1){
      fprintf(ficresvpl,"******\n");                      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);
      varpl=matrix(1,nlstate,(int) bage, (int) fage);                    }
      oldm=oldms;savm=savms;                    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);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                    /*printf(fignu*/
    }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
  }                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
   fclose(ficresvpl);                      first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
   /*---------- End : free ----------------*/                      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);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);                      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>\
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  %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);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                      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);
   free_matrix(matcov,1,npar,1,npar);                      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",\
   free_vector(delti,1,npar);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                                mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                    }else{
                       first=0;
   printf("End of Imach\n");                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */                      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);
   /* 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);*/                      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",\
   /*printf("Total time was %d uSec.\n", total_usecs);*/                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   /*------ End -----------*/                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
  end:                } /* end loop age */
 #ifdef windows                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
  chdir(pathcd);                first=1;
 #endif              } /*l12 */
              } /* k12 */
  system("..\\gp37mgw\\wgnuplot graph.plt");          } /*l1 */
         }/* k1 */
 #ifdef windows      } /* loop covariates */
   while (z[0] != 'q') {    }
     chdir(pathcd);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     scanf("%s",z);    free_vector(xp,1,npar);
     if (z[0] == 'c') system("./imach");    fclose(ficresprob);
     else if (z[0] == 'e') {    fclose(ficresprobcov);
       chdir(path);    fclose(ficresprobcor);
       system(optionfilehtm);    fflush(ficgp);
     }    fflush(fichtmcov);
     else if (z[0] == 'q') exit(0);  }
   }  
 #endif  
 }  /******************* 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 */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i]==1 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i]==0 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         if (wav[i]>1 & agecens[i]>15) {
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov){
     int i;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
         for(j=0; line[j] != '\n';j++){  /* Untabifies line */
           if(line[j] == '\t')
             line[j] = ' ';
         }
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of 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); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (j=1; j<=lastpass; j++)
           if (s[j][i]>nlstate) {
             dcwave[i]=j;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];agecens[i]=1.; 
           if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
           cens[i]=1;
           
           if (ageexmed[i]<1) cens[i]=-1;
           if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
   
       p[1]=0.1; p[2]=0.1;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow-mort"); 
     strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
     /*  for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     */
     fprintf(ficrespow,"\n");
   
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM,delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov);
     } /* Endof if mle==-3 */
   
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficrespl,"#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 ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\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,"\"");
     strcat(plotcmd,pathimach);
     strcat(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd,"\"");
     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') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

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  Added in v.1.103


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