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version 1.22, 2002/02/22 17:54:20 version 1.95, 2003/07/08 07:54:34
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 /* $Id$  /* $Id$
    Interpolate Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.95  2003/07/08 07:54:34  brouard
      * imach.c (Repository):
   This program computes Healthy Life Expectancies from    (Repository): Using imachwizard code to output a more meaningful covariance
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    matrix (cov(a12,c31) instead of numbers.
   first survey ("cross") where individuals from different ages are  
   interviewed on their health status or degree of disability (in the    Revision 1.94  2003/06/27 13:00:02  brouard
   case of a health survey which is our main interest) -2- at least a    Just cleaning
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.93  2003/06/25 16:33:55  brouard
   computed from the time spent in each health state according to a    (Module): On windows (cygwin) function asctime_r doesn't
   model. More health states you consider, more time is necessary to reach the    exist so I changed back to asctime which exists.
   Maximum Likelihood of the parameters involved in the model.  The    (Module): Version 0.96b
   simplest model is the multinomial logistic model where pij is the  
   probabibility to be observed in state j at the second wave    Revision 1.92  2003/06/25 16:30:45  brouard
   conditional to be observed in state i at the first wave. Therefore    (Module): On windows (cygwin) function asctime_r doesn't
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    exist so I changed back to asctime which exists.
   '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    Revision 1.91  2003/06/25 15:30:29  brouard
   where the markup *Covariates have to be included here again* invites    * imach.c (Repository): Duplicated warning errors corrected.
   you to do it.  More covariates you add, slower the    (Repository): Elapsed time after each iteration is now output. It
   convergence.    helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
   The advantage of this computer programme, compared to a simple    concerning matrix of covariance. It has extension -cov.htm.
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.90  2003/06/24 12:34:15  brouard
   intermediate interview, the information is lost, but taken into    (Module): Some bugs corrected for windows. Also, when
   account using an interpolation or extrapolation.      mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    Revision 1.89  2003/06/24 12:30:52  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    (Module): Some bugs corrected for windows. Also, when
   states. This elementary transition (by month or quarter trimester,    mle=-1 a template is output in file "or"mypar.txt with the design
   semester or year) is model as a multinomial logistic.  The hPx    of the covariance matrix to be input.
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.88  2003/06/23 17:54:56  brouard
   hPijx.    * 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.
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.87  2003/06/18 12:26:01  brouard
   of the life expectancies. It also computes the prevalence limits.    Version 0.96
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.86  2003/06/17 20:04:08  brouard
            Institut national d'études démographiques, Paris.    (Module): Change position of html and gnuplot routines and added
   This software have been partly granted by Euro-REVES, a concerted action    routine fileappend.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.85  2003/06/17 13:12:43  brouard
   software can be distributed freely for non commercial use. Latest version    * imach.c (Repository): Check when date of death was earlier that
   can be accessed at http://euroreves.ined.fr/imach .    current date of interview. It may happen when the death was just
   **********************************************************************/    prior to the death. In this case, dh was negative and likelihood
      was wrong (infinity). We still send an "Error" but patch by
 #include <math.h>    assuming that the date of death was just one stepm after the
 #include <stdio.h>    interview.
 #include <stdlib.h>    (Repository): Because some people have very long ID (first column)
 #include <unistd.h>    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 MAXLINE 256    truncation)
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    (Repository): No more line truncation errors.
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.84  2003/06/13 21:44:43  brouard
 #define windows    * imach.c (Repository): Replace "freqsummary" at a correct
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    place. It differs from routine "prevalence" which may be called
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    many times. Probs is memory consuming and must be used with
     parcimony.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.83  2003/06/10 13:39:11  lievre
 #define NINTERVMAX 8    *** empty log message ***
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.82  2003/06/05 15:57:20  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    Add log in  imach.c and  fullversion number is now printed.
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */  */
 #define AGESUP 130  /*
 #define AGEBASE 40     Interpolated Markov Chain
   
     Short summary of the programme:
 int erreur; /* Error number */    
 int nvar;    This program computes Healthy Life Expectancies from
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 int npar=NPARMAX;    first survey ("cross") where individuals from different ages are
 int nlstate=2; /* Number of live states */    interviewed on their health status or degree of disability (in the
 int ndeath=1; /* Number of dead states */    case of a health survey which is our main interest) -2- at least a
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    second wave of interviews ("longitudinal") which measure each change
 int popbased=0;    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
 int *wav; /* Number of waves for this individuual 0 is possible */    model. More health states you consider, more time is necessary to reach the
 int maxwav; /* Maxim number of waves */    Maximum Likelihood of the parameters involved in the model.  The
 int jmin, jmax; /* min, max spacing between 2 waves */    simplest model is the multinomial logistic model where pij is the
 int mle, weightopt;    probability to be observed in state j at the second wave
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    conditional to be observed in state i at the first wave. Therefore
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 double jmean; /* Mean space between 2 waves */    'age' is age and 'sex' is a covariate. If you want to have a more
 double **oldm, **newm, **savm; /* Working pointers to matrices */    complex model than "constant and age", you should modify the program
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    where the markup *Covariates have to be included here again* invites
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    you to do it.  More covariates you add, slower the
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    convergence.
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    The advantage of this computer programme, compared to a simple
  FILE  *ficresvij;    multinomial logistic model, is clear when the delay between waves is not
   char fileresv[FILENAMELENGTH];    identical for each individual. Also, if a individual missed an
  FILE  *ficresvpl;    intermediate interview, the information is lost, but taken into
   char fileresvpl[FILENAMELENGTH];    account using an interpolation or extrapolation.  
   
 #define NR_END 1    hPijx is the probability to be observed in state i at age x+h
 #define FREE_ARG char*    conditional to the observed state i at age x. The delay 'h' can be
 #define FTOL 1.0e-10    split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
 #define NRANSI    semester or year) is modelled as a multinomial logistic.  The hPx
 #define ITMAX 200    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
 #define TOL 2.0e-4    hPijx.
   
 #define CGOLD 0.3819660    Also this programme outputs the covariance matrix of the parameters but also
 #define ZEPS 1.0e-10    of the life expectancies. It also computes the stable prevalence. 
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #define GOLD 1.618034             Institut national d'études démographiques, Paris.
 #define GLIMIT 100.0    This software have been partly granted by Euro-REVES, a concerted action
 #define TINY 1.0e-20    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
 static double maxarg1,maxarg2;    software can be distributed freely for non commercial use. Latest version
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    can be accessed at http://euroreves.ined.fr/imach .
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #define rint(a) floor(a+0.5)    
     **********************************************************************/
 static double sqrarg;  /*
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    main
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    read parameterfile
     read datafile
 int imx;    concatwav
 int stepm;    freqsummary
 /* Stepm, step in month: minimum step interpolation*/    if (mle >= 1)
       mlikeli
 int m,nb;    print results files
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    if mle==1 
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;       computes hessian
 double **pmmij, ***probs, ***mobaverage;    read end of parameter file: agemin, agemax, bage, fage, estepm
 double dateintmean=0;        begin-prev-date,...
     open gnuplot file
 double *weight;    open html file
 int **s; /* Status */    stable prevalence
 double *agedc, **covar, idx;     for age prevalim()
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    h Pij x
     variance of p varprob
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    forecasting if prevfcast==1 prevforecast call prevalence()
 double ftolhess; /* Tolerance for computing hessian */    health expectancies
     Variance-covariance of DFLE
 /**************** split *************************/    prevalence()
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )     movingaverage()
 {    varevsij() 
    char *s;                             /* pointer */    if popbased==1 varevsij(,popbased)
    int  l1, l2;                         /* length counters */    total life expectancies
     Variance of stable prevalence
    l1 = strlen( path );                 /* length of path */   end
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  */
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */  
 #else  
    s = strrchr( path, '/' );            /* find last / */   
 #endif  #include <math.h>
    if ( s == NULL ) {                   /* no directory, so use current */  #include <stdio.h>
 #if     defined(__bsd__)                /* get current working directory */  #include <stdlib.h>
       extern char       *getwd( );  #include <unistd.h>
   
       if ( getwd( dirc ) == NULL ) {  #include <sys/time.h>
 #else  #include <time.h>
       extern char       *getcwd( );  #include "timeval.h"
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  /* #include <libintl.h> */
 #endif  /* #define _(String) gettext (String) */
          return( GLOCK_ERROR_GETCWD );  
       }  #define MAXLINE 256
       strcpy( name, path );             /* we've got it */  #define GNUPLOTPROGRAM "gnuplot"
    } else {                             /* strip direcotry from path */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       s++;                              /* after this, the filename */  #define FILENAMELENGTH 132
       l2 = strlen( s );                 /* length of filename */  /*#define DEBUG*/
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  /*#define windows*/
       strcpy( name, s );                /* save file name */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       dirc[l1-l2] = 0;                  /* add zero */  
    }  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
    l1 = strlen( dirc );                 /* length of directory */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #define NINTERVMAX 8
 #else  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #endif  #define NCOVMAX 8 /* Maximum number of covariates */
    s = strrchr( name, '.' );            /* find last / */  #define MAXN 20000
    s++;  #define YEARM 12. /* Number of months per year */
    strcpy(ext,s);                       /* save extension */  #define AGESUP 130
    l1= strlen( name);  #define AGEBASE 40
    l2= strlen( s)+1;  #ifdef unix
    strncpy( finame, name, l1-l2);  #define DIRSEPARATOR '/'
    finame[l1-l2]= 0;  #define ODIRSEPARATOR '\\'
    return( 0 );                         /* we're done */  #else
 }  #define DIRSEPARATOR '\\'
   #define ODIRSEPARATOR '/'
   #endif
 /******************************************/  
   /* $Id$ */
 void replace(char *s, char*t)  /* $State$ */
 {  
   int i;  char version[]="Imach version 0.96b, June 2003, INED-EUROREVES ";
   int lg=20;  char fullversion[]="$Revision$ $Date$"; 
   i=0;  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   lg=strlen(t);  int nvar;
   for(i=0; i<= lg; i++) {  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
     (s[i] = t[i]);  int npar=NPARMAX;
     if (t[i]== '\\') s[i]='/';  int nlstate=2; /* Number of live states */
   }  int ndeath=1; /* Number of dead states */
 }  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
 int nbocc(char *s, char occ)  
 {  int *wav; /* Number of waves for this individuual 0 is possible */
   int i,j=0;  int maxwav; /* Maxim number of waves */
   int lg=20;  int jmin, jmax; /* min, max spacing between 2 waves */
   i=0;  int gipmx, gsw; /* Global variables on the number of contributions 
   lg=strlen(s);                     to the likelihood and the sum of weights (done by funcone)*/
   for(i=0; i<= lg; i++) {  int mle, weightopt;
   if  (s[i] == occ ) j++;  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 */
   return j;  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. */
   double jmean; /* Mean space between 2 waves */
 void cutv(char *u,char *v, char*t, char occ)  double **oldm, **newm, **savm; /* Working pointers to matrices */
 {  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   int i,lg,j,p=0;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   i=0;  FILE *ficlog, *ficrespow;
   for(j=0; j<=strlen(t)-1; j++) {  int globpr; /* Global variable for printing or not */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  double fretone; /* Only one call to likelihood */
   }  long ipmx; /* Number of contributions */
   double sw; /* Sum of weights */
   lg=strlen(t);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   for(j=0; j<p; j++) {  FILE *ficresilk;
     (u[j] = t[j]);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   }  FILE *ficresprobmorprev;
      u[p]='\0';  FILE *fichtm, *fichtmcov; /* Html File */
   FILE *ficreseij;
    for(j=0; j<= lg; j++) {  char filerese[FILENAMELENGTH];
     if (j>=(p+1))(v[j-p-1] = t[j]);  FILE  *ficresvij;
   }  char fileresv[FILENAMELENGTH];
 }  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
 /********************** nrerror ********************/  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 void nrerror(char error_text[])  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 {  char tmpout[FILENAMELENGTH]; 
   fprintf(stderr,"ERREUR ...\n");  char command[FILENAMELENGTH];
   fprintf(stderr,"%s\n",error_text);  int  outcmd=0;
   exit(1);  
 }  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 /*********************** vector *******************/  
 double *vector(int nl, int nh)  char filelog[FILENAMELENGTH]; /* Log file */
 {  char filerest[FILENAMELENGTH];
   double *v;  char fileregp[FILENAMELENGTH];
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  char popfile[FILENAMELENGTH];
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 }  
   struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 /************************ free vector ******************/  struct timezone tzp;
 void free_vector(double*v, int nl, int nh)  extern int gettimeofday();
 {  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   free((FREE_ARG)(v+nl-NR_END));  long time_value;
 }  extern long time();
   char strcurr[80], strfor[80];
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  #define NR_END 1
 {  #define FREE_ARG char*
   int *v;  #define FTOL 1.0e-10
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  #define NRANSI 
   return v-nl+NR_END;  #define ITMAX 200 
 }  
   #define TOL 2.0e-4 
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)  #define CGOLD 0.3819660 
 {  #define ZEPS 1.0e-10 
   free((FREE_ARG)(v+nl-NR_END));  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 }  
   #define GOLD 1.618034 
 /******************* imatrix *******************************/  #define GLIMIT 100.0 
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #define TINY 1.0e-20 
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {  static double maxarg1,maxarg2;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   int **m;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
      
   /* allocate pointers to rows */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #define rint(a) floor(a+0.5)
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  static double sqrarg;
   m -= nrl;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
    #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
    
   /* allocate rows and set pointers to them */  int imx; 
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  int stepm;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /* Stepm, step in month: minimum step interpolation*/
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  int estepm;
    /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    int m,nb;
   /* return pointer to array of pointers to rows */  long *num;
   return m;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 }  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
 /****************** free_imatrix *************************/  double dateintmean=0;
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  double *weight;
       long nch,ncl,nrh,nrl;  int **s; /* Status */
      /* free an int matrix allocated by imatrix() */  double *agedc, **covar, idx;
 {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 }  double ftolhess; /* Tolerance for computing hessian */
   
 /******************* matrix *******************************/  /**************** split *************************/
 double **matrix(long nrl, long nrh, long ncl, long nch)  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 {  {
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    char  *ss;                            /* pointer */
   double **m;    int   l1, l2;                         /* length counters */
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    l1 = strlen(path );                   /* length of path */
   if (!m) nrerror("allocation failure 1 in matrix()");    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   m += NR_END;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   m -= nrl;    if ( ss == NULL ) {                   /* no directory, so use current */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      /* get current working directory */
   m[nrl] += NR_END;      /*    extern  char* getcwd ( char *buf , int len);*/
   m[nrl] -= ncl;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         return( GLOCK_ERROR_GETCWD );
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;      }
   return m;      strcpy( name, path );               /* we've got it */
 }    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
 /*************************free matrix ************************/      l2 = strlen( ss );                  /* length of filename */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 {      strcpy( name, ss );         /* save file name */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   free((FREE_ARG)(m+nrl-NR_END));      dirc[l1-l2] = 0;                    /* add zero */
 }    }
     l1 = strlen( dirc );                  /* length of directory */
 /******************* ma3x *******************************/    /*#ifdef windows
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 {  #else
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   double ***m;  #endif
     */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    ss = strrchr( name, '.' );            /* find last / */
   if (!m) nrerror("allocation failure 1 in matrix()");    ss++;
   m += NR_END;    strcpy(ext,ss);                       /* save extension */
   m -= nrl;    l1= strlen( name);
     l2= strlen(ss)+1;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    strncpy( finame, name, l1-l2);
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    finame[l1-l2]= 0;
   m[nrl] += NR_END;    return( 0 );                          /* we're done */
   m[nrl] -= ncl;  }
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   /******************************************/
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  void replace_back_to_slash(char *s, char*t)
   m[nrl][ncl] += NR_END;  {
   m[nrl][ncl] -= nll;    int i;
   for (j=ncl+1; j<=nch; j++)    int lg=0;
     m[nrl][j]=m[nrl][j-1]+nlay;    i=0;
      lg=strlen(t);
   for (i=nrl+1; i<=nrh; i++) {    for(i=0; i<= lg; i++) {
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;      (s[i] = t[i]);
     for (j=ncl+1; j<=nch; j++)      if (t[i]== '\\') s[i]='/';
       m[i][j]=m[i][j-1]+nlay;    }
   }  }
   return m;  
 }  int nbocc(char *s, char occ)
   {
 /*************************free ma3x ************************/    int i,j=0;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    int lg=20;
 {    i=0;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    lg=strlen(s);
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    for(i=0; i<= lg; i++) {
   free((FREE_ARG)(m+nrl-NR_END));    if  (s[i] == occ ) j++;
 }    }
     return j;
 /***************** f1dim *************************/  }
 extern int ncom;  
 extern double *pcom,*xicom;  void cutv(char *u,char *v, char*t, char occ)
 extern double (*nrfunc)(double []);  {
      /* cuts string t into u and v where u is ended by char occ excluding it
 double f1dim(double x)       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 {       gives u="abcedf" and v="ghi2j" */
   int j;    int i,lg,j,p=0;
   double f;    i=0;
   double *xt;    for(j=0; j<=strlen(t)-1; j++) {
        if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   xt=vector(1,ncom);    }
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);    lg=strlen(t);
   free_vector(xt,1,ncom);    for(j=0; j<p; j++) {
   return f;      (u[j] = t[j]);
 }    }
        u[p]='\0';
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)     for(j=0; j<= lg; j++) {
 {      if (j>=(p+1))(v[j-p-1] = t[j]);
   int iter;    }
   double a,b,d,etemp;  }
   double fu,fv,fw,fx;  
   double ftemp;  /********************** nrerror ********************/
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  void nrerror(char error_text[])
    {
   a=(ax < cx ? ax : cx);    fprintf(stderr,"ERREUR ...\n");
   b=(ax > cx ? ax : cx);    fprintf(stderr,"%s\n",error_text);
   x=w=v=bx;    exit(EXIT_FAILURE);
   fw=fv=fx=(*f)(x);  }
   for (iter=1;iter<=ITMAX;iter++) {  /*********************** vector *******************/
     xm=0.5*(a+b);  double *vector(int nl, int nh)
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  {
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    double *v;
     printf(".");fflush(stdout);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 #ifdef DEBUG    if (!v) nrerror("allocation failure in vector");
     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);    return v-nl+NR_END;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  }
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  /************************ free vector ******************/
       *xmin=x;  void free_vector(double*v, int nl, int nh)
       return fx;  {
     }    free((FREE_ARG)(v+nl-NR_END));
     ftemp=fu;  }
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);  /************************ivector *******************************/
       q=(x-v)*(fx-fw);  int *ivector(long nl,long nh)
       p=(x-v)*q-(x-w)*r;  {
       q=2.0*(q-r);    int *v;
       if (q > 0.0) p = -p;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       q=fabs(q);    if (!v) nrerror("allocation failure in ivector");
       etemp=e;    return v-nl+NR_END;
       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));  /******************free ivector **************************/
       else {  void free_ivector(int *v, long nl, long nh)
         d=p/q;  {
         u=x+d;    free((FREE_ARG)(v+nl-NR_END));
         if (u-a < tol2 || b-u < tol2)  }
           d=SIGN(tol1,xm-x);  
       }  /************************lvector *******************************/
     } else {  long *lvector(long nl,long nh)
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  {
     }    long *v;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     fu=(*f)(u);    if (!v) nrerror("allocation failure in ivector");
     if (fu <= fx) {    return v-nl+NR_END;
       if (u >= x) a=x; else b=x;  }
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  /******************free lvector **************************/
         } else {  void free_lvector(long *v, long nl, long nh)
           if (u < x) a=u; else b=u;  {
           if (fu <= fw || w == x) {    free((FREE_ARG)(v+nl-NR_END));
             v=w;  }
             w=u;  
             fv=fw;  /******************* imatrix *******************************/
             fw=fu;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
           } else if (fu <= fv || v == x || v == w) {       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
             v=u;  { 
             fv=fu;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
           }    int **m; 
         }    
   }    /* allocate pointers to rows */ 
   nrerror("Too many iterations in brent");    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   *xmin=x;    if (!m) nrerror("allocation failure 1 in matrix()"); 
   return fx;    m += NR_END; 
 }    m -= nrl; 
     
 /****************** mnbrak ***********************/    
     /* allocate rows and set pointers to them */ 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
             double (*func)(double))    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 {    m[nrl] += NR_END; 
   double ulim,u,r,q, dum;    m[nrl] -= ncl; 
   double fu;    
      for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   *fa=(*func)(*ax);    
   *fb=(*func)(*bx);    /* return pointer to array of pointers to rows */ 
   if (*fb > *fa) {    return m; 
     SHFT(dum,*ax,*bx,dum)  } 
       SHFT(dum,*fb,*fa,dum)  
       }  /****************** free_imatrix *************************/
   *cx=(*bx)+GOLD*(*bx-*ax);  void free_imatrix(m,nrl,nrh,ncl,nch)
   *fc=(*func)(*cx);        int **m;
   while (*fb > *fc) {        long nch,ncl,nrh,nrl; 
     r=(*bx-*ax)*(*fb-*fc);       /* free an int matrix allocated by imatrix() */ 
     q=(*bx-*cx)*(*fb-*fa);  { 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    free((FREE_ARG) (m+nrl-NR_END)); 
     ulim=(*bx)+GLIMIT*(*cx-*bx);  } 
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);  /******************* matrix *******************************/
     } else if ((*cx-u)*(u-ulim) > 0.0) {  double **matrix(long nrl, long nrh, long ncl, long nch)
       fu=(*func)(u);  {
       if (fu < *fc) {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    double **m;
           SHFT(*fb,*fc,fu,(*func)(u))  
           }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    if (!m) nrerror("allocation failure 1 in matrix()");
       u=ulim;    m += NR_END;
       fu=(*func)(u);    m -= nrl;
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       fu=(*func)(u);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     }    m[nrl] += NR_END;
     SHFT(*ax,*bx,*cx,u)    m[nrl] -= ncl;
       SHFT(*fa,*fb,*fc,fu)  
       }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 }    return m;
     /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
 /*************** linmin ************************/     */
   }
 int ncom;  
 double *pcom,*xicom;  /*************************free matrix ************************/
 double (*nrfunc)(double []);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
    {
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 {    free((FREE_ARG)(m+nrl-NR_END));
   double brent(double ax, double bx, double cx,  }
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);  /******************* ma3x *******************************/
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
               double *fc, double (*func)(double));  {
   int j;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   double xx,xmin,bx,ax;    double ***m;
   double fx,fb,fa;  
      m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   ncom=n;    if (!m) nrerror("allocation failure 1 in matrix()");
   pcom=vector(1,n);    m += NR_END;
   xicom=vector(1,n);    m -= nrl;
   nrfunc=func;  
   for (j=1;j<=n;j++) {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     pcom[j]=p[j];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     xicom[j]=xi[j];    m[nrl] += NR_END;
   }    m[nrl] -= ncl;
   ax=0.0;  
   xx=1.0;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 #ifdef DEBUG    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    m[nrl][ncl] += NR_END;
 #endif    m[nrl][ncl] -= nll;
   for (j=1;j<=n;j++) {    for (j=ncl+1; j<=nch; j++) 
     xi[j] *= xmin;      m[nrl][j]=m[nrl][j-1]+nlay;
     p[j] += xi[j];    
   }    for (i=nrl+1; i<=nrh; i++) {
   free_vector(xicom,1,n);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   free_vector(pcom,1,n);      for (j=ncl+1; j<=nch; j++) 
 }        m[i][j]=m[i][j-1]+nlay;
     }
 /*************** powell ************************/    return m; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
             double (*func)(double []))             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 {    */
   void linmin(double p[], double xi[], int n, double *fret,  }
               double (*func)(double []));  
   int i,ibig,j;  /*************************free ma3x ************************/
   double del,t,*pt,*ptt,*xit;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   double fp,fptt;  {
   double *xits;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   pt=vector(1,n);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   ptt=vector(1,n);    free((FREE_ARG)(m+nrl-NR_END));
   xit=vector(1,n);  }
   xits=vector(1,n);  
   *fret=(*func)(p);  /*************** function subdirf ***********/
   for (j=1;j<=n;j++) pt[j]=p[j];  char *subdirf(char fileres[])
   for (*iter=1;;++(*iter)) {  {
     fp=(*fret);    /* Caution optionfilefiname is hidden */
     ibig=0;    strcpy(tmpout,optionfilefiname);
     del=0.0;    strcat(tmpout,"/"); /* Add to the right */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    strcat(tmpout,fileres);
     for (i=1;i<=n;i++)    return tmpout;
       printf(" %d %.12f",i, p[i]);  }
     printf("\n");  
     for (i=1;i<=n;i++) {  /*************** function subdirf2 ***********/
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  char *subdirf2(char fileres[], char *preop)
       fptt=(*fret);  {
 #ifdef DEBUG    
       printf("fret=%lf \n",*fret);    /* Caution optionfilefiname is hidden */
 #endif    strcpy(tmpout,optionfilefiname);
       printf("%d",i);fflush(stdout);    strcat(tmpout,"/");
       linmin(p,xit,n,fret,func);    strcat(tmpout,preop);
       if (fabs(fptt-(*fret)) > del) {    strcat(tmpout,fileres);
         del=fabs(fptt-(*fret));    return tmpout;
         ibig=i;  }
       }  
 #ifdef DEBUG  /*************** function subdirf3 ***********/
       printf("%d %.12e",i,(*fret));  char *subdirf3(char fileres[], char *preop, char *preop2)
       for (j=1;j<=n;j++) {  {
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    
         printf(" x(%d)=%.12e",j,xit[j]);    /* Caution optionfilefiname is hidden */
       }    strcpy(tmpout,optionfilefiname);
       for(j=1;j<=n;j++)    strcat(tmpout,"/");
         printf(" p=%.12e",p[j]);    strcat(tmpout,preop);
       printf("\n");    strcat(tmpout,preop2);
 #endif    strcat(tmpout,fileres);
     }    return tmpout;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  }
 #ifdef DEBUG  
       int k[2],l;  /***************** f1dim *************************/
       k[0]=1;  extern int ncom; 
       k[1]=-1;  extern double *pcom,*xicom;
       printf("Max: %.12e",(*func)(p));  extern double (*nrfunc)(double []); 
       for (j=1;j<=n;j++)   
         printf(" %.12e",p[j]);  double f1dim(double x) 
       printf("\n");  { 
       for(l=0;l<=1;l++) {    int j; 
         for (j=1;j<=n;j++) {    double f;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    double *xt; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);   
         }    xt=vector(1,ncom); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       }    f=(*nrfunc)(xt); 
 #endif    free_vector(xt,1,ncom); 
     return f; 
   } 
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  /*****************brent *************************/
       free_vector(ptt,1,n);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       free_vector(pt,1,n);  { 
       return;    int iter; 
     }    double a,b,d,etemp;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    double fu,fv,fw,fx;
     for (j=1;j<=n;j++) {    double ftemp;
       ptt[j]=2.0*p[j]-pt[j];    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       xit[j]=p[j]-pt[j];    double e=0.0; 
       pt[j]=p[j];   
     }    a=(ax < cx ? ax : cx); 
     fptt=(*func)(ptt);    b=(ax > cx ? ax : cx); 
     if (fptt < fp) {    x=w=v=bx; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    fw=fv=fx=(*f)(x); 
       if (t < 0.0) {    for (iter=1;iter<=ITMAX;iter++) { 
         linmin(p,xit,n,fret,func);      xm=0.5*(a+b); 
         for (j=1;j<=n;j++) {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
           xi[j][ibig]=xi[j][n];      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
           xi[j][n]=xit[j];      printf(".");fflush(stdout);
         }      fprintf(ficlog,".");fflush(ficlog);
 #ifdef DEBUG  #ifdef DEBUG
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      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(j=1;j<=n;j++)      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);
           printf(" %.12e",xit[j]);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
         printf("\n");  #endif
 #endif      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       }        *xmin=x; 
     }        return fx; 
   }      } 
 }      ftemp=fu;
       if (fabs(e) > tol1) { 
 /**** Prevalence limit ****************/        r=(x-w)*(fx-fv); 
         q=(x-v)*(fx-fw); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        p=(x-v)*q-(x-w)*r; 
 {        q=2.0*(q-r); 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        if (q > 0.0) p = -p; 
      matrix by transitions matrix until convergence is reached */        q=fabs(q); 
         etemp=e; 
   int i, ii,j,k;        e=d; 
   double min, max, maxmin, maxmax,sumnew=0.;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   double **matprod2();          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double **out, cov[NCOVMAX], **pmij();        else { 
   double **newm;          d=p/q; 
   double agefin, delaymax=50 ; /* Max number of years to converge */          u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
   for (ii=1;ii<=nlstate+ndeath;ii++)            d=SIGN(tol1,xm-x); 
     for (j=1;j<=nlstate+ndeath;j++){        } 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      } else { 
     }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
    cov[1]=1.;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
        fu=(*f)(u); 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      if (fu <= fx) { 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        if (u >= x) a=x; else b=x; 
     newm=savm;        SHFT(v,w,x,u) 
     /* Covariates have to be included here again */          SHFT(fv,fw,fx,fu) 
      cov[2]=agefin;          } else { 
              if (u < x) a=u; else b=u; 
       for (k=1; k<=cptcovn;k++) {            if (fu <= fw || w == x) { 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];              v=w; 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/              w=u; 
       }              fv=fw; 
       for (k=1; k<=cptcovage;k++)              fw=fu; 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];            } else if (fu <= fv || v == x || v == w) { 
       for (k=1; k<=cptcovprod;k++)              v=u; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];              fv=fu; 
             } 
       /*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]);*/    } 
     nrerror("Too many iterations in brent"); 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    *xmin=x; 
     return fx; 
     savm=oldm;  } 
     oldm=newm;  
     maxmax=0.;  /****************** mnbrak ***********************/
     for(j=1;j<=nlstate;j++){  
       min=1.;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       max=0.;              double (*func)(double)) 
       for(i=1; i<=nlstate; i++) {  { 
         sumnew=0;    double ulim,u,r,q, dum;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    double fu; 
         prlim[i][j]= newm[i][j]/(1-sumnew);   
         max=FMAX(max,prlim[i][j]);    *fa=(*func)(*ax); 
         min=FMIN(min,prlim[i][j]);    *fb=(*func)(*bx); 
       }    if (*fb > *fa) { 
       maxmin=max-min;      SHFT(dum,*ax,*bx,dum) 
       maxmax=FMAX(maxmax,maxmin);        SHFT(dum,*fb,*fa,dum) 
     }        } 
     if(maxmax < ftolpl){    *cx=(*bx)+GOLD*(*bx-*ax); 
       return prlim;    *fc=(*func)(*cx); 
     }    while (*fb > *fc) { 
   }      r=(*bx-*ax)*(*fb-*fc); 
 }      q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 /*************** transition probabilities ***************/        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      if ((*bx-u)*(u-*cx) > 0.0) { 
 {        fu=(*func)(u); 
   double s1, s2;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   /*double t34;*/        fu=(*func)(u); 
   int i,j,j1, nc, ii, jj;        if (fu < *fc) { 
           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     for(i=1; i<= nlstate; i++){            SHFT(*fb,*fc,fu,(*func)(u)) 
     for(j=1; j<i;j++){            } 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         /*s2 += param[i][j][nc]*cov[nc];*/        u=ulim; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        fu=(*func)(u); 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      } else { 
       }        u=(*cx)+GOLD*(*cx-*bx); 
       ps[i][j]=s2;        fu=(*func)(u); 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      } 
     }      SHFT(*ax,*bx,*cx,u) 
     for(j=i+1; j<=nlstate+ndeath;j++){        SHFT(*fa,*fb,*fc,fu) 
       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];  } 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  
       }  /*************** linmin ************************/
       ps[i][j]=s2;  
     }  int ncom; 
   }  double *pcom,*xicom;
     /*ps[3][2]=1;*/  double (*nrfunc)(double []); 
    
   for(i=1; i<= nlstate; i++){  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
      s1=0;  { 
     for(j=1; j<i; j++)    double brent(double ax, double bx, double cx, 
       s1+=exp(ps[i][j]);                 double (*f)(double), double tol, double *xmin); 
     for(j=i+1; j<=nlstate+ndeath; j++)    double f1dim(double x); 
       s1+=exp(ps[i][j]);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     ps[i][i]=1./(s1+1.);                double *fc, double (*func)(double)); 
     for(j=1; j<i; j++)    int j; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    double xx,xmin,bx,ax; 
     for(j=i+1; j<=nlstate+ndeath; j++)    double fx,fb,fa;
       ps[i][j]= exp(ps[i][j])*ps[i][i];   
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    ncom=n; 
   } /* end i */    pcom=vector(1,n); 
     xicom=vector(1,n); 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    nrfunc=func; 
     for(jj=1; jj<= nlstate+ndeath; jj++){    for (j=1;j<=n;j++) { 
       ps[ii][jj]=0;      pcom[j]=p[j]; 
       ps[ii][ii]=1;      xicom[j]=xi[j]; 
     }    } 
   }    ax=0.0; 
     xx=1.0; 
     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     for(jj=1; jj<= nlstate+ndeath; jj++){  #ifdef DEBUG
      printf("%lf ",ps[ii][jj]);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
    }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     printf("\n ");  #endif
     }    for (j=1;j<=n;j++) { 
     printf("\n ");printf("%lf ",cov[2]);*/      xi[j] *= xmin; 
 /*      p[j] += xi[j]; 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    } 
   goto end;*/    free_vector(xicom,1,n); 
     return ps;    free_vector(pcom,1,n); 
 }  } 
   
 /**************** Product of 2 matrices ******************/  char *asc_diff_time(long time_sec, char ascdiff[])
   {
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    long sec_left, days, hours, minutes;
 {    days = (time_sec) / (60*60*24);
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    sec_left = (time_sec) % (60*60*24);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    hours = (sec_left) / (60*60) ;
   /* in, b, out are matrice of pointers which should have been initialized    sec_left = (sec_left) %(60*60);
      before: only the contents of out is modified. The function returns    minutes = (sec_left) /60;
      a pointer to pointers identical to out */    sec_left = (sec_left) % (60);
   long i, j, k;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   for(i=nrl; i<= nrh; i++)    return ascdiff;
     for(k=ncolol; k<=ncoloh; k++)  }
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];  /*************** powell ************************/
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   return out;              double (*func)(double [])) 
 }  { 
     void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
 /************* Higher Matrix Product ***************/    int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    double fp,fptt;
 {    double *xits;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    int niterf, itmp;
      duration (i.e. until  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    pt=vector(1,n); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    ptt=vector(1,n); 
      (typically every 2 years instead of every month which is too big).    xit=vector(1,n); 
      Model is determined by parameters x and covariates have to be    xits=vector(1,n); 
      included manually here.    *fret=(*func)(p); 
     for (j=1;j<=n;j++) pt[j]=p[j]; 
      */    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
   int i, j, d, h, k;      ibig=0; 
   double **out, cov[NCOVMAX];      del=0.0; 
   double **newm;      last_time=curr_time;
       (void) gettimeofday(&curr_time,&tzp);
   /* Hstepm could be zero and should return the unit matrix */      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
   for (i=1;i<=nlstate+ndeath;i++)      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);
     for (j=1;j<=nlstate+ndeath;j++){      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       oldm[i][j]=(i==j ? 1.0 : 0.0);      for (i=1;i<=n;i++) {
       po[i][j][0]=(i==j ? 1.0 : 0.0);        printf(" %d %.12f",i, p[i]);
     }        fprintf(ficlog," %d %.12lf",i, p[i]);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        fprintf(ficrespow," %.12lf", p[i]);
   for(h=1; h <=nhstepm; h++){      }
     for(d=1; d <=hstepm; d++){      printf("\n");
       newm=savm;      fprintf(ficlog,"\n");
       /* Covariates have to be included here again */      fprintf(ficrespow,"\n");fflush(ficrespow);
       cov[1]=1.;      if(*iter <=3){
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        tm = *localtime(&curr_time.tv_sec);
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        strcpy(strcurr,asctime(&tmf));
       for (k=1; k<=cptcovage;k++)  /*       asctime_r(&tm,strcurr); */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        forecast_time=curr_time;
       for (k=1; k<=cptcovprod;k++)        itmp = strlen(strcurr);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        if(strcurr[itmp-1]=='\n')
           strcurr[itmp-1]='\0';
         printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        for(niterf=10;niterf<=30;niterf+=10){
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
                    pmij(pmmij,cov,ncovmodel,x,nlstate));          tmf = *localtime(&forecast_time.tv_sec);
       savm=oldm;  /*      asctime_r(&tmf,strfor); */
       oldm=newm;          strcpy(strfor,asctime(&tmf));
     }          itmp = strlen(strfor);
     for(i=1; i<=nlstate+ndeath; i++)          if(strfor[itmp-1]=='\n')
       for(j=1;j<=nlstate+ndeath;j++) {          strfor[itmp-1]='\0';
         po[i][j][h]=newm[i][j];          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
          */        }
       }      }
   } /* end h */      for (i=1;i<=n;i++) { 
   return po;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
 }        fptt=(*fret); 
   #ifdef DEBUG
         printf("fret=%lf \n",*fret);
 /*************** log-likelihood *************/        fprintf(ficlog,"fret=%lf \n",*fret);
 double func( double *x)  #endif
 {        printf("%d",i);fflush(stdout);
   int i, ii, j, k, mi, d, kk;        fprintf(ficlog,"%d",i);fflush(ficlog);
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        linmin(p,xit,n,fret,func); 
   double **out;        if (fabs(fptt-(*fret)) > del) { 
   double sw; /* Sum of weights */          del=fabs(fptt-(*fret)); 
   double lli; /* Individual log likelihood */          ibig=i; 
   long ipmx;        } 
   /*extern weight */  #ifdef DEBUG
   /* We are differentiating ll according to initial status */        printf("%d %.12e",i,(*fret));
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        fprintf(ficlog,"%d %.12e",i,(*fret));
   /*for(i=1;i<imx;i++)        for (j=1;j<=n;j++) {
     printf(" %d\n",s[4][i]);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   */          printf(" x(%d)=%.12e",j,xit[j]);
   cov[1]=1.;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }
   for(k=1; k<=nlstate; k++) ll[k]=0.;        for(j=1;j<=n;j++) {
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){          printf(" p=%.12e",p[j]);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];          fprintf(ficlog," p=%.12e",p[j]);
     for(mi=1; mi<= wav[i]-1; mi++){        }
       for (ii=1;ii<=nlstate+ndeath;ii++)        printf("\n");
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        fprintf(ficlog,"\n");
       for(d=0; d<dh[mi][i]; d++){  #endif
         newm=savm;      } 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         for (kk=1; kk<=cptcovage;kk++) {  #ifdef DEBUG
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        int k[2],l;
         }        k[0]=1;
                k[1]=-1;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        printf("Max: %.12e",(*func)(p));
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        fprintf(ficlog,"Max: %.12e",(*func)(p));
         savm=oldm;        for (j=1;j<=n;j++) {
         oldm=newm;          printf(" %.12e",p[j]);
                  fprintf(ficlog," %.12e",p[j]);
                }
       } /* end mult */        printf("\n");
              fprintf(ficlog,"\n");
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        for(l=0;l<=1;l++) {
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          for (j=1;j<=n;j++) {
       ipmx +=1;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       sw += weight[i];            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     } /* end of wave */          }
   } /* end of individual */          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        }
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  #endif
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  
   return -l;  
 }        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
 /*********** Maximum Likelihood Estimation ***************/        free_vector(pt,1,n); 
         return; 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      } 
 {      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   int i,j, iter;      for (j=1;j<=n;j++) { 
   double **xi,*delti;        ptt[j]=2.0*p[j]-pt[j]; 
   double fret;        xit[j]=p[j]-pt[j]; 
   xi=matrix(1,npar,1,npar);        pt[j]=p[j]; 
   for (i=1;i<=npar;i++)      } 
     for (j=1;j<=npar;j++)      fptt=(*func)(ptt); 
       xi[i][j]=(i==j ? 1.0 : 0.0);      if (fptt < fp) { 
   printf("Powell\n");        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   powell(p,xi,npar,ftol,&iter,&fret,func);        if (t < 0.0) { 
           linmin(p,xit,n,fret,func); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          for (j=1;j<=n;j++) { 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));            xi[j][ibig]=xi[j][n]; 
             xi[j][n]=xit[j]; 
 }          }
   #ifdef DEBUG
 /**** Computes Hessian and covariance matrix ***/          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 {          for(j=1;j<=n;j++){
   double  **a,**y,*x,pd;            printf(" %.12e",xit[j]);
   double **hess;            fprintf(ficlog," %.12e",xit[j]);
   int i, j,jk;          }
   int *indx;          printf("\n");
           fprintf(ficlog,"\n");
   double hessii(double p[], double delta, int theta, double delti[]);  #endif
   double hessij(double p[], double delti[], int i, int j);        }
   void lubksb(double **a, int npar, int *indx, double b[]) ;      } 
   void ludcmp(double **a, int npar, int *indx, double *d) ;    } 
   } 
   hess=matrix(1,npar,1,npar);  
   /**** Prevalence limit (stable prevalence)  ****************/
   printf("\nCalculation of the hessian matrix. Wait...\n");  
   for (i=1;i<=npar;i++){  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     printf("%d",i);fflush(stdout);  {
     hess[i][i]=hessii(p,ftolhess,i,delti);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     /*printf(" %f ",p[i]);*/       matrix by transitions matrix until convergence is reached */
     /*printf(" %lf ",hess[i][i]);*/  
   }    int i, ii,j,k;
      double min, max, maxmin, maxmax,sumnew=0.;
   for (i=1;i<=npar;i++) {    double **matprod2();
     for (j=1;j<=npar;j++)  {    double **out, cov[NCOVMAX], **pmij();
       if (j>i) {    double **newm;
         printf(".%d%d",i,j);fflush(stdout);    double agefin, delaymax=50 ; /* Max number of years to converge */
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];        for (ii=1;ii<=nlstate+ndeath;ii++)
         /*printf(" %lf ",hess[i][j]);*/      for (j=1;j<=nlstate+ndeath;j++){
       }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }      }
   }  
   printf("\n");     cov[1]=1.;
    
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
      for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   a=matrix(1,npar,1,npar);      newm=savm;
   y=matrix(1,npar,1,npar);      /* Covariates have to be included here again */
   x=vector(1,npar);       cov[2]=agefin;
   indx=ivector(1,npar);    
   for (i=1;i<=npar;i++)        for (k=1; k<=cptcovn;k++) {
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   ludcmp(a,npar,indx,&pd);          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
         }
   for (j=1;j<=npar;j++) {        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for (i=1;i<=npar;i++) x[i]=0;        for (k=1; k<=cptcovprod;k++)
     x[j]=1;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       matcov[i][j]=x[i];        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     }        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   }      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
   printf("\n#Hessian matrix#\n");      savm=oldm;
   for (i=1;i<=npar;i++) {      oldm=newm;
     for (j=1;j<=npar;j++) {      maxmax=0.;
       printf("%.3e ",hess[i][j]);      for(j=1;j<=nlstate;j++){
     }        min=1.;
     printf("\n");        max=0.;
   }        for(i=1; i<=nlstate; i++) {
           sumnew=0;
   /* Recompute Inverse */          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   for (i=1;i<=npar;i++)          prlim[i][j]= newm[i][j]/(1-sumnew);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          max=FMAX(max,prlim[i][j]);
   ludcmp(a,npar,indx,&pd);          min=FMIN(min,prlim[i][j]);
         }
   /*  printf("\n#Hessian matrix recomputed#\n");        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
   for (j=1;j<=npar;j++) {      }
     for (i=1;i<=npar;i++) x[i]=0;      if(maxmax < ftolpl){
     x[j]=1;        return prlim;
     lubksb(a,npar,indx,x);      }
     for (i=1;i<=npar;i++){    }
       y[i][j]=x[i];  }
       printf("%.3e ",y[i][j]);  
     }  /*************** transition probabilities ***************/ 
     printf("\n");  
   }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   */  {
     double s1, s2;
   free_matrix(a,1,npar,1,npar);    /*double t34;*/
   free_matrix(y,1,npar,1,npar);    int i,j,j1, nc, ii, jj;
   free_vector(x,1,npar);  
   free_ivector(indx,1,npar);      for(i=1; i<= nlstate; i++){
   free_matrix(hess,1,npar,1,npar);      for(j=1; j<i;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           /*s2 += param[i][j][nc]*cov[nc];*/
 }          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
 /*************** hessian matrix ****************/        }
 double hessii( double x[], double delta, int theta, double delti[])        ps[i][j]=s2;
 {        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   int i;      }
   int l=1, lmax=20;      for(j=i+1; j<=nlstate+ndeath;j++){
   double k1,k2;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   double p2[NPARMAX+1];          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   double res;          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        }
   double fx;        ps[i][j]=s2;
   int k=0,kmax=10;      }
   double l1;    }
       /*ps[3][2]=1;*/
   fx=func(x);  
   for (i=1;i<=npar;i++) p2[i]=x[i];    for(i=1; i<= nlstate; i++){
   for(l=0 ; l <=lmax; l++){       s1=0;
     l1=pow(10,l);      for(j=1; j<i; j++)
     delts=delt;        s1+=exp(ps[i][j]);
     for(k=1 ; k <kmax; k=k+1){      for(j=i+1; j<=nlstate+ndeath; j++)
       delt = delta*(l1*k);        s1+=exp(ps[i][j]);
       p2[theta]=x[theta] +delt;      ps[i][i]=1./(s1+1.);
       k1=func(p2)-fx;      for(j=1; j<i; j++)
       p2[theta]=x[theta]-delt;        ps[i][j]= exp(ps[i][j])*ps[i][i];
       k2=func(p2)-fx;      for(j=i+1; j<=nlstate+ndeath; j++)
       /*res= (k1-2.0*fx+k2)/delt/delt; */        ps[i][j]= exp(ps[i][j])*ps[i][i];
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
          } /* end i */
 #ifdef DEBUG  
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
 #endif      for(jj=1; jj<= nlstate+ndeath; jj++){
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        ps[ii][jj]=0;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        ps[ii][ii]=1;
         k=kmax;      }
       }    }
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  
         k=kmax; l=lmax*10.;  
       }    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      for(jj=1; jj<= nlstate+ndeath; jj++){
         delts=delt;       printf("%lf ",ps[ii][jj]);
       }     }
     }      printf("\n ");
   }      }
   delti[theta]=delts;      printf("\n ");printf("%lf ",cov[2]);*/
   return res;  /*
      for(i=1; i<= npar; i++) printf("%f ",x[i]);
 }    goto end;*/
       return ps;
 double hessij( double x[], double delti[], int thetai,int thetaj)  }
 {  
   int i;  /**************** Product of 2 matrices ******************/
   int l=1, l1, lmax=20;  
   double k1,k2,k3,k4,res,fx;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   double p2[NPARMAX+1];  {
   int k;    /* 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(...) */
   fx=func(x);    /* in, b, out are matrice of pointers which should have been initialized 
   for (k=1; k<=2; k++) {       before: only the contents of out is modified. The function returns
     for (i=1;i<=npar;i++) p2[i]=x[i];       a pointer to pointers identical to out */
     p2[thetai]=x[thetai]+delti[thetai]/k;    long i, j, k;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    for(i=nrl; i<= nrh; i++)
     k1=func(p2)-fx;      for(k=ncolol; k<=ncoloh; k++)
          for(j=ncl,out[i][k]=0.; j<=nch; j++)
     p2[thetai]=x[thetai]+delti[thetai]/k;          out[i][k] +=in[i][j]*b[j][k];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k2=func(p2)-fx;    return out;
    }
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k3=func(p2)-fx;  /************* Higher Matrix Product ***************/
    
     p2[thetai]=x[thetai]-delti[thetai]/k;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  {
     k4=func(p2)-fx;    /* Computes the transition matrix starting at age 'age' over 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */       'nhstepm*hstepm*stepm' months (i.e. until
 #ifdef DEBUG       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     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);       nhstepm*hstepm matrices. 
 #endif       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 
   return res;       for the memory).
 }       Model is determined by parameters x and covariates have to be 
        included manually here. 
 /************** Inverse of matrix **************/  
 void ludcmp(double **a, int n, int *indx, double *d)       */
 {  
   int i,imax,j,k;    int i, j, d, h, k;
   double big,dum,sum,temp;    double **out, cov[NCOVMAX];
   double *vv;    double **newm;
    
   vv=vector(1,n);    /* Hstepm could be zero and should return the unit matrix */
   *d=1.0;    for (i=1;i<=nlstate+ndeath;i++)
   for (i=1;i<=n;i++) {      for (j=1;j<=nlstate+ndeath;j++){
     big=0.0;        oldm[i][j]=(i==j ? 1.0 : 0.0);
     for (j=1;j<=n;j++)        po[i][j][0]=(i==j ? 1.0 : 0.0);
       if ((temp=fabs(a[i][j])) > big) big=temp;      }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     vv[i]=1.0/big;    for(h=1; h <=nhstepm; h++){
   }      for(d=1; d <=hstepm; d++){
   for (j=1;j<=n;j++) {        newm=savm;
     for (i=1;i<j;i++) {        /* Covariates have to be included here again */
       sum=a[i][j];        cov[1]=1.;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       a[i][j]=sum;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     }        for (k=1; k<=cptcovage;k++)
     big=0.0;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for (i=j;i<=n;i++) {        for (k=1; k<=cptcovprod;k++)
       sum=a[i][j];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       for (k=1;k<j;k++)  
         sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       if ( (dum=vv[i]*fabs(sum)) >= big) {        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         big=dum;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         imax=i;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
       }        savm=oldm;
     }        oldm=newm;
     if (j != imax) {      }
       for (k=1;k<=n;k++) {      for(i=1; i<=nlstate+ndeath; i++)
         dum=a[imax][k];        for(j=1;j<=nlstate+ndeath;j++) {
         a[imax][k]=a[j][k];          po[i][j][h]=newm[i][j];
         a[j][k]=dum;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       }           */
       *d = -(*d);        }
       vv[imax]=vv[j];    } /* end h */
     }    return po;
     indx[j]=imax;  }
     if (a[j][j] == 0.0) a[j][j]=TINY;  
     if (j != n) {  
       dum=1.0/(a[j][j]);  /*************** log-likelihood *************/
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  double func( double *x)
     }  {
   }    int i, ii, j, k, mi, d, kk;
   free_vector(vv,1,n);  /* Doesn't work */    double l, ll[NLSTATEMAX], cov[NCOVMAX];
 ;    double **out;
 }    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
 void lubksb(double **a, int n, int *indx, double b[])    int s1, s2;
 {    double bbh, survp;
   int i,ii=0,ip,j;    long ipmx;
   double sum;    /*extern weight */
      /* We are differentiating ll according to initial status */
   for (i=1;i<=n;i++) {    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     ip=indx[i];    /*for(i=1;i<imx;i++) 
     sum=b[ip];      printf(" %d\n",s[4][i]);
     b[ip]=b[i];    */
     if (ii)    cov[1]=1.;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  
     else if (sum) ii=i;    for(k=1; k<=nlstate; k++) ll[k]=0.;
     b[i]=sum;  
   }    if(mle==1){
   for (i=n;i>=1;i--) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     sum=b[i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        for(mi=1; mi<= wav[i]-1; mi++){
     b[i]=sum/a[i][i];          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
 }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
 /************ Frequencies ********************/            }
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2)          for(d=0; d<dh[mi][i]; d++){
 {  /* Some frequencies */            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;            for (kk=1; kk<=cptcovage;kk++) {
   double ***freq; /* Frequencies */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double *pp;            }
   double pos, k2, dateintsum=0,k2cpt=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   FILE *ficresp;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   char fileresp[FILENAMELENGTH];            savm=oldm;
             oldm=newm;
   pp=vector(1,nlstate);          } /* end mult */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        
   strcpy(fileresp,"p");          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   strcat(fileresp,fileres);          /* But now since version 0.9 we anticipate for bias and large stepm.
   if((ficresp=fopen(fileresp,"w"))==NULL) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     printf("Problem with prevalence resultfile: %s\n", fileresp);           * (in months) between two waves is not a multiple of stepm, we rounded to 
     exit(0);           * the nearest (and in case of equal distance, to the lowest) interval but now
   }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   j1=0;           * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   j=cptcoveff;           * -stepm/2 to stepm/2 .
   if (cptcovn<1) {j=1;ncodemax[1]=1;}           * For stepm=1 the results are the same as for previous versions of Imach.
            * For stepm > 1 the results are less biased than in previous versions. 
   for(k1=1; k1<=j;k1++){           */
    for(i1=1; i1<=ncodemax[k1];i1++){          s1=s[mw[mi][i]][i];
        j1++;          s2=s[mw[mi+1][i]][i];
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          bbh=(double)bh[mi][i]/(double)stepm; 
          scanf("%d", i);*/          /* bias is positive if real duration
         for (i=-1; i<=nlstate+ndeath; i++)             * is higher than the multiple of stepm and negative otherwise.
          for (jk=-1; jk<=nlstate+ndeath; jk++)             */
            for(m=agemin; m <= agemax+3; m++)          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
              freq[i][jk][m]=0;          if( s2 > nlstate){ 
             /* i.e. if s2 is a death state and if the date of death is known then the contribution
         dateintsum=0;               to the likelihood is the probability to die between last step unit time and current 
         k2cpt=0;               step unit time, which is also the differences between probability to die before dh 
        for (i=1; i<=imx; i++) {               and probability to die before dh-stepm . 
          bool=1;               In version up to 0.92 likelihood was computed
          if  (cptcovn>0) {          as if date of death was unknown. Death was treated as any other
            for (z1=1; z1<=cptcoveff; z1++)          health state: the date of the interview describes the actual state
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          and not the date of a change in health state. The former idea was
                bool=0;          to consider that at each interview the state was recorded
          }          (healthy, disable or death) and IMaCh was corrected; but when we
          if (bool==1) {          introduced the exact date of death then we should have modified
            for(m=firstpass; m<=lastpass; m++){          the contribution of an exact death to the likelihood. This new
              k2=anint[m][i]+(mint[m][i]/12.);          contribution is smaller and very dependent of the step unit
              if ((k2>=dateprev1) && (k2<=dateprev2)) {          stepm. It is no more the probability to die between last interview
                if(agev[m][i]==0) agev[m][i]=agemax+1;          and month of death but the probability to survive from last
                if(agev[m][i]==1) agev[m][i]=agemax+2;          interview up to one month before death multiplied by the
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          probability to die within a month. Thanks to Chris
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          Jackson for correcting this bug.  Former versions increased
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          mortality artificially. The bad side is that we add another loop
                  dateintsum=dateintsum+k2;          which slows down the processing. The difference can be up to 10%
                  k2cpt++;          lower mortality.
                }            */
             lli=log(out[s1][s2] - savm[s1][s2]);
              }          }else{
            }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
          }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
        }          } 
         if  (cptcovn>0) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
          fprintf(ficresp, "\n#********** Variable ");          /*if(lli ==000.0)*/
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          /*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); */
        fprintf(ficresp, "**********\n#");          ipmx +=1;
         }          sw += weight[i];
        for(i=1; i<=nlstate;i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        } /* end of wave */
        fprintf(ficresp, "\n");      } /* end of individual */
            }  else if(mle==2){
   for(i=(int)agemin; i <= (int)agemax+3; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     if(i==(int)agemax+3)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       printf("Total");        for(mi=1; mi<= wav[i]-1; mi++){
     else          for (ii=1;ii<=nlstate+ndeath;ii++)
       printf("Age %d", 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++) {
       if(pp[jk]>=1.e-10)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            }
       else            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
             oldm=newm;
      for(jk=1; jk <=nlstate ; jk++){          } /* end mult */
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        
         pp[jk] += freq[jk][m][i];          s1=s[mw[mi][i]][i];
      }          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
     for(jk=1,pos=0; jk <=nlstate ; jk++)          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 */
       pos += pp[jk];          ipmx +=1;
     for(jk=1; jk <=nlstate ; jk++){          sw += weight[i];
       if(pos>=1.e-5)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        } /* end of wave */
       else      } /* end of individual */
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    }  else if(mle==3){  /* exponential inter-extrapolation */
       if( i <= (int) agemax){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         if(pos>=1.e-5){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        for(mi=1; mi<= wav[i]-1; mi++){
           probs[i][jk][j1]= pp[jk]/pos;          for (ii=1;ii<=nlstate+ndeath;ii++)
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/            for (j=1;j<=nlstate+ndeath;j++){
         }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       else              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            }
       }          for(d=0; d<dh[mi][i]; d++){
     }            newm=savm;
     for(jk=-1; jk <=nlstate+ndeath; jk++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(m=-1; m <=nlstate+ndeath; m++)            for (kk=1; kk<=cptcovage;kk++) {
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     if(i <= (int) agemax)            }
       fprintf(ficresp,"\n");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     printf("\n");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
     }            oldm=newm;
  }          } /* end mult */
   dateintmean=dateintsum/k2cpt;        
            s1=s[mw[mi][i]][i];
   fclose(ficresp);          s2=s[mw[mi+1][i]][i];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          bbh=(double)bh[mi][i]/(double)stepm; 
   free_vector(pp,1,nlstate);          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
           ipmx +=1;
   /* End of Freq */          sw += weight[i];
 }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
 /************ Prevalence ********************/      } /* end of individual */
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)    }else if (mle==4){  /* ml=4 no inter-extrapolation */
 {  /* Some frequencies */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        for(mi=1; mi<= wav[i]-1; mi++){
   double ***freq; /* Frequencies */          for (ii=1;ii<=nlstate+ndeath;ii++)
   double *pp;            for (j=1;j<=nlstate+ndeath;j++){
   double pos, k2;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   pp=vector(1,nlstate);            }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   j1=0;            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   j=cptcoveff;            }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
  for(k1=1; k1<=j;k1++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(i1=1; i1<=ncodemax[k1];i1++){            savm=oldm;
       j1++;            oldm=newm;
            } /* end mult */
       for (i=-1; i<=nlstate+ndeath; i++)          
         for (jk=-1; jk<=nlstate+ndeath; jk++)            s1=s[mw[mi][i]][i];
           for(m=agemin; m <= agemax+3; m++)          s2=s[mw[mi+1][i]][i];
             freq[i][jk][m]=0;          if( s2 > nlstate){ 
                  lli=log(out[s1][s2] - savm[s1][s2]);
       for (i=1; i<=imx; i++) {          }else{
         bool=1;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         if  (cptcovn>0) {          }
           for (z1=1; z1<=cptcoveff; z1++)          ipmx +=1;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          sw += weight[i];
               bool=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         }  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         if (bool==1) {        } /* end of wave */
           for(m=firstpass; m<=lastpass; m++){      } /* end of individual */
             k2=anint[m][i]+(mint[m][i]/12.);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
               if(agev[m][i]==0) agev[m][i]=agemax+1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
               if(agev[m][i]==1) agev[m][i]=agemax+2;        for(mi=1; mi<= wav[i]-1; mi++){
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          for (ii=1;ii<=nlstate+ndeath;ii++)
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];              for (j=1;j<=nlstate+ndeath;j++){
             }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            }
       }          for(d=0; d<dh[mi][i]; d++){
                  newm=savm;
         for(i=(int)agemin; i <= (int)agemax+3; i++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for(jk=1; jk <=nlstate ; jk++){            for (kk=1; kk<=cptcovage;kk++) {
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
               pp[jk] += freq[jk][m][i];            }
           }          
           for(jk=1; jk <=nlstate ; jk++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             for(m=-1, pos=0; m <=0 ; m++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             pos += freq[jk][m][i];            savm=oldm;
         }            oldm=newm;
                  } /* end mult */
          for(jk=1; jk <=nlstate ; jk++){        
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          s1=s[mw[mi][i]][i];
              pp[jk] += freq[jk][m][i];          s2=s[mw[mi+1][i]][i];
          }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                    ipmx +=1;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          for(jk=1; jk <=nlstate ; jk++){                    /*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( i <= (int) agemax){        } /* end of wave */
              if(pos>=1.e-5){      } /* end of individual */
                probs[i][jk][j1]= pp[jk]/pos;    } /* End of if */
              }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
            }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
          }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
              return -l;
         }  }
     }  
   }  /*************** log-likelihood *************/
    double funcone( double *x)
    {
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    /* Same as likeli but slower because of a lot of printf and if */
   free_vector(pp,1,nlstate);    int i, ii, j, k, mi, d, kk;
      double l, ll[NLSTATEMAX], cov[NCOVMAX];
 }  /* End of Freq */    double **out;
     double lli; /* Individual log likelihood */
 /************* Waves Concatenation ***************/    double llt;
     int s1, s2;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    double bbh, survp;
 {    /*extern weight */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    /* We are differentiating ll according to initial status */
      Death is a valid wave (if date is known).    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    /*for(i=1;i<imx;i++) 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      printf(" %d\n",s[4][i]);
      and mw[mi+1][i]. dh depends on stepm.    */
      */    cov[1]=1.;
   
   int i, mi, m;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  
      double sum=0., jmean=0.;*/    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int j, k=0,jk, ju, jl;      for(mi=1; mi<= wav[i]-1; mi++){
   double sum=0.;        for (ii=1;ii<=nlstate+ndeath;ii++)
   jmin=1e+5;          for (j=1;j<=nlstate+ndeath;j++){
   jmax=-1;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   jmean=0.;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for(i=1; i<=imx; i++){          }
     mi=0;        for(d=0; d<dh[mi][i]; d++){
     m=firstpass;          newm=savm;
     while(s[m][i] <= nlstate){          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if(s[m][i]>=1)          for (kk=1; kk<=cptcovage;kk++) {
         mw[++mi][i]=m;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       if(m >=lastpass)          }
         break;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       else                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         m++;          savm=oldm;
     }/* end while */          oldm=newm;
     if (s[m][i] > nlstate){        } /* end mult */
       mi++;     /* Death is another wave */        
       /* if(mi==0)  never been interviewed correctly before death */        s1=s[mw[mi][i]][i];
          /* Only death is a correct wave */        s2=s[mw[mi+1][i]][i];
       mw[mi][i]=m;        bbh=(double)bh[mi][i]/(double)stepm; 
     }        /* bias is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.
     wav[i]=mi;         */
     if(mi==0)        if( s2 > nlstate && (mle <5) ){  /* Jackson */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          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 */
   for(i=1; i<=imx; i++){        } else if(mle==2){
     for(mi=1; mi<wav[i];mi++){          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       if (stepm <=0)        } else if(mle==3){  /* exponential inter-extrapolation */
         dh[mi][i]=1;          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       else{        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         if (s[mw[mi+1][i]][i] > nlstate) {          lli=log(out[s1][s2]); /* Original formula */
           if (agedc[i] < 2*AGESUP) {        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          lli=log(out[s1][s2]); /* Original formula */
           if(j==0) j=1;  /* Survives at least one month after exam */        } /* End of if */
           k=k+1;        ipmx +=1;
           if (j >= jmax) jmax=j;        sw += weight[i];
           if (j <= jmin) jmin=j;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           sum=sum+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]); */
           /* if (j<10) printf("j=%d num=%d ",j,i); */        if(globpr){
           }          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
         }   %10.6f %10.6f %10.6f ", \
         else{                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           k=k+1;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
           if (j >= jmax) jmax=j;            llt +=ll[k]*gipmx/gsw;
           else if (j <= jmin)jmin=j;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          }
           sum=sum+j;          fprintf(ficresilk," %10.6f\n", -llt);
         }        }
         jk= j/stepm;      } /* end of wave */
         jl= j -jk*stepm;    } /* end of individual */
         ju= j -(jk+1)*stepm;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         if(jl <= -ju)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           dh[mi][i]=jk;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         else    if(globpr==0){ /* First time we count the contributions and weights */
           dh[mi][i]=jk+1;      gipmx=ipmx;
         if(dh[mi][i]==0)      gsw=sw;
           dh[mi][i]=1; /* At least one step */    }
       }    return -l;
     }  }
   }  
   jmean=sum/k;  
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  /*************** function likelione ***********/
  }  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
 /*********** Tricode ****************************/  {
 void tricode(int *Tvar, int **nbcode, int imx)    /* This routine should help understanding what is done with 
 {       the selection of individuals/waves and
   int Ndum[20],ij=1, k, j, i;       to check the exact contribution to the likelihood.
   int cptcode=0;       Plotting could be done.
   cptcoveff=0;     */
      int k;
   for (k=0; k<19; k++) Ndum[k]=0;  
   for (k=1; k<=7; k++) ncodemax[k]=0;    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      strcat(fileresilk,fileres);
     for (i=1; i<=imx; i++) {      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       ij=(int)(covar[Tvar[j]][i]);        printf("Problem with resultfile: %s\n", fileresilk);
       Ndum[ij]++;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      }
       if (ij > cptcode) cptcode=ij;      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");
     }      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 (i=0; i<=cptcode; i++) {      for(k=1; k<=nlstate; k++) 
       if(Ndum[i]!=0) ncodemax[j]++;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     }      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     ij=1;    }
   
     *fretone=(*funcone)(p);
     for (i=1; i<=ncodemax[j]; i++) {    if(*globpri !=0){
       for (k=0; k<=19; k++) {      fclose(ficresilk);
         if (Ndum[k] != 0) {      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
           nbcode[Tvar[j]][ij]=k;      fflush(fichtm); 
           ij++;    } 
         }    return;
         if (ij > ncodemax[j]) break;  }
       }    
     }  
   }    /*********** Maximum Likelihood Estimation ***************/
   
  for (k=0; k<19; k++) Ndum[k]=0;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
  for (i=1; i<=ncovmodel-2; i++) {    int i,j, iter;
       ij=Tvar[i];    double **xi;
       Ndum[ij]++;    double fret;
     }    double fretone; /* Only one call to likelihood */
     char filerespow[FILENAMELENGTH];
  ij=1;    xi=matrix(1,npar,1,npar);
  for (i=1; i<=10; i++) {    for (i=1;i<=npar;i++)
    if((Ndum[i]!=0) && (i<=ncov)){      for (j=1;j<=npar;j++)
      Tvaraff[ij]=i;        xi[i][j]=(i==j ? 1.0 : 0.0);
      ij++;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
    }    strcpy(filerespow,"pow"); 
  }    strcat(filerespow,fileres);
      if((ficrespow=fopen(filerespow,"w"))==NULL) {
     cptcoveff=ij-1;      printf("Problem with resultfile: %s\n", filerespow);
 }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
 /*********** Health Expectancies ****************/    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)      for(j=1;j<=nlstate+ndeath;j++)
 {        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   /* Health expectancies */    fprintf(ficrespow,"\n");
   int i, j, nhstepm, hstepm, h;  
   double age, agelim,hf;    powell(p,xi,npar,ftol,&iter,&fret,func);
   double ***p3mat;  
      fclose(ficrespow);
   fprintf(ficreseij,"# Health expectancies\n");    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   fprintf(ficreseij,"# Age");    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   for(i=1; i<=nlstate;i++)    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for(j=1; j<=nlstate;j++)  
       fprintf(ficreseij," %1d-%1d",i,j);  }
   fprintf(ficreseij,"\n");  
   /**** Computes Hessian and covariance matrix ***/
   hstepm=1*YEARM; /*  Every j years of age (in month) */  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  {
     double  **a,**y,*x,pd;
   agelim=AGESUP;    double **hess;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    int i, j,jk;
     /* nhstepm age range expressed in number of stepm */    int *indx;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years = 20*12/6=40 stepm */    double hessii(double p[], double delta, int theta, double delti[]);
     if (stepm >= YEARM) hstepm=1;    double hessij(double p[], double delti[], int i, int j);
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    void lubksb(double **a, int npar, int *indx, double b[]) ;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    void ludcmp(double **a, int npar, int *indx, double *d) ;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    hess=matrix(1,npar,1,npar);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    
     printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for(i=1; i<=nlstate;i++)    for (i=1;i<=npar;i++){
       for(j=1; j<=nlstate;j++)      printf("%d",i);fflush(stdout);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){      fprintf(ficlog,"%d",i);fflush(ficlog);
           eij[i][j][(int)age] +=p3mat[i][j][h];      hess[i][i]=hessii(p,ftolhess,i,delti);
         }      /*printf(" %f ",p[i]);*/
          /*printf(" %lf ",hess[i][i]);*/
     hf=1;    }
     if (stepm >= YEARM) hf=stepm/YEARM;    
     fprintf(ficreseij,"%.0f",age );    for (i=1;i<=npar;i++) {
     for(i=1; i<=nlstate;i++)      for (j=1;j<=npar;j++)  {
       for(j=1; j<=nlstate;j++){        if (j>i) { 
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          printf(".%d%d",i,j);fflush(stdout);
       }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     fprintf(ficreseij,"\n");          hess[i][j]=hessij(p,delti,i,j);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          hess[j][i]=hess[i][j];    
   }          /*printf(" %lf ",hess[i][j]);*/
 }        }
       }
 /************ 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)    printf("\n");
 {    fprintf(ficlog,"\n");
   /* Variance of health expectancies */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   double **newm;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   double **dnewm,**doldm;    
   int i, j, nhstepm, hstepm, h;    a=matrix(1,npar,1,npar);
   int k, cptcode;    y=matrix(1,npar,1,npar);
   double *xp;    x=vector(1,npar);
   double **gp, **gm;    indx=ivector(1,npar);
   double ***gradg, ***trgradg;    for (i=1;i<=npar;i++)
   double ***p3mat;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   double age,agelim;    ludcmp(a,npar,indx,&pd);
   int theta;  
     for (j=1;j<=npar;j++) {
    fprintf(ficresvij,"# Covariances of life expectancies\n");      for (i=1;i<=npar;i++) x[i]=0;
   fprintf(ficresvij,"# Age");      x[j]=1;
   for(i=1; i<=nlstate;i++)      lubksb(a,npar,indx,x);
     for(j=1; j<=nlstate;j++)      for (i=1;i<=npar;i++){ 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        matcov[i][j]=x[i];
   fprintf(ficresvij,"\n");      }
     }
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);    printf("\n#Hessian matrix#\n");
   doldm=matrix(1,nlstate,1,nlstate);    fprintf(ficlog,"\n#Hessian matrix#\n");
      for (i=1;i<=npar;i++) { 
   hstepm=1*YEARM; /* Every year of age */      for (j=1;j<=npar;j++) { 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        printf("%.3e ",hess[i][j]);
   agelim = AGESUP;        fprintf(ficlog,"%.3e ",hess[i][j]);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      printf("\n");
     if (stepm >= YEARM) hstepm=1;      fprintf(ficlog,"\n");
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    /* Recompute Inverse */
     gp=matrix(0,nhstepm,1,nlstate);    for (i=1;i<=npar;i++)
     gm=matrix(0,nhstepm,1,nlstate);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */    /*  printf("\n#Hessian matrix recomputed#\n");
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }    for (j=1;j<=npar;j++) {
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for (i=1;i<=npar;i++) x[i]=0;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      x[j]=1;
       lubksb(a,npar,indx,x);
       if (popbased==1) {      for (i=1;i<=npar;i++){ 
         for(i=1; i<=nlstate;i++)        y[i][j]=x[i];
           prlim[i][i]=probs[(int)age][i][ij];        printf("%.3e ",y[i][j]);
       }        fprintf(ficlog,"%.3e ",y[i][j]);
            }
       for(j=1; j<= nlstate; j++){      printf("\n");
         for(h=0; h<=nhstepm; h++){      fprintf(ficlog,"\n");
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    }
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    */
         }  
       }    free_matrix(a,1,npar,1,npar);
        free_matrix(y,1,npar,1,npar);
       for(i=1; i<=npar; i++) /* Computes gradient */    free_vector(x,1,npar);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    free_ivector(indx,1,npar);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      free_matrix(hess,1,npar,1,npar);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
   
       if (popbased==1) {  }
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];  /*************** hessian matrix ****************/
       }  double hessii( double x[], double delta, int theta, double delti[])
   {
       for(j=1; j<= nlstate; j++){    int i;
         for(h=0; h<=nhstepm; h++){    int l=1, lmax=20;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    double k1,k2;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    double p2[NPARMAX+1];
         }    double res;
       }    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
       for(j=1; j<= nlstate; j++)    int k=0,kmax=10;
         for(h=0; h<=nhstepm; h++){    double l1;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  
         }    fx=func(x);
     } /* End theta */    for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      l1=pow(10,l);
       delts=delt;
     for(h=0; h<=nhstepm; h++)      for(k=1 ; k <kmax; k=k+1){
       for(j=1; j<=nlstate;j++)        delt = delta*(l1*k);
         for(theta=1; theta <=npar; theta++)        p2[theta]=x[theta] +delt;
           trgradg[h][j][theta]=gradg[h][theta][j];        k1=func(p2)-fx;
         p2[theta]=x[theta]-delt;
     for(i=1;i<=nlstate;i++)        k2=func(p2)-fx;
       for(j=1;j<=nlstate;j++)        /*res= (k1-2.0*fx+k2)/delt/delt; */
         vareij[i][j][(int)age] =0.;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     for(h=0;h<=nhstepm;h++){        
       for(k=0;k<=nhstepm;k++){  #ifdef DEBUG
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        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);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         for(i=1;i<=nlstate;i++)  #endif
           for(j=1;j<=nlstate;j++)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
             vareij[i][j][(int)age] += doldm[i][j];        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       }          k=kmax;
     }        }
     h=1;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     if (stepm >= YEARM) h=stepm/YEARM;          k=kmax; l=lmax*10.;
     fprintf(ficresvij,"%.0f ",age );        }
     for(i=1; i<=nlstate;i++)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       for(j=1; j<=nlstate;j++){          delts=delt;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);        }
       }      }
     fprintf(ficresvij,"\n");    }
     free_matrix(gp,0,nhstepm,1,nlstate);    delti[theta]=delts;
     free_matrix(gm,0,nhstepm,1,nlstate);    return res; 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */  double hessij( double x[], double delti[], int thetai,int thetaj)
    {
   free_vector(xp,1,npar);    int i;
   free_matrix(doldm,1,nlstate,1,npar);    int l=1, l1, lmax=20;
   free_matrix(dnewm,1,nlstate,1,nlstate);    double k1,k2,k3,k4,res,fx;
     double p2[NPARMAX+1];
 }    int k;
   
 /************ Variance of prevlim ******************/    fx=func(x);
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    for (k=1; k<=2; k++) {
 {      for (i=1;i<=npar;i++) p2[i]=x[i];
   /* Variance of prevalence limit */      p2[thetai]=x[thetai]+delti[thetai]/k;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double **newm;      k1=func(p2)-fx;
   double **dnewm,**doldm;    
   int i, j, nhstepm, hstepm;      p2[thetai]=x[thetai]+delti[thetai]/k;
   int k, cptcode;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   double *xp;      k2=func(p2)-fx;
   double *gp, *gm;    
   double **gradg, **trgradg;      p2[thetai]=x[thetai]-delti[thetai]/k;
   double age,agelim;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   int theta;      k3=func(p2)-fx;
        
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      p2[thetai]=x[thetai]-delti[thetai]/k;
   fprintf(ficresvpl,"# Age");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   for(i=1; i<=nlstate;i++)      k4=func(p2)-fx;
       fprintf(ficresvpl," %1d-%1d",i,i);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   fprintf(ficresvpl,"\n");  #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);
   xp=vector(1,npar);      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);
   dnewm=matrix(1,nlstate,1,npar);  #endif
   doldm=matrix(1,nlstate,1,nlstate);    }
      return res;
   hstepm=1*YEARM; /* Every year of age */  }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   agelim = AGESUP;  /************** Inverse of matrix **************/
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  void ludcmp(double **a, int n, int *indx, double *d) 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  { 
     if (stepm >= YEARM) hstepm=1;    int i,imax,j,k; 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    double big,dum,sum,temp; 
     gradg=matrix(1,npar,1,nlstate);    double *vv; 
     gp=vector(1,nlstate);   
     gm=vector(1,nlstate);    vv=vector(1,n); 
     *d=1.0; 
     for(theta=1; theta <=npar; theta++){    for (i=1;i<=n;i++) { 
       for(i=1; i<=npar; i++){ /* Computes gradient */      big=0.0; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      for (j=1;j<=n;j++) 
       }        if ((temp=fabs(a[i][j])) > big) big=temp; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       for(i=1;i<=nlstate;i++)      vv[i]=1.0/big; 
         gp[i] = prlim[i][i];    } 
        for (j=1;j<=n;j++) { 
       for(i=1; i<=npar; i++) /* Computes gradient */      for (i=1;i<j;i++) { 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        sum=a[i][j]; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       for(i=1;i<=nlstate;i++)        a[i][j]=sum; 
         gm[i] = prlim[i][i];      } 
       big=0.0; 
       for(i=1;i<=nlstate;i++)      for (i=j;i<=n;i++) { 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        sum=a[i][j]; 
     } /* End theta */        for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
     trgradg =matrix(1,nlstate,1,npar);        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
     for(j=1; j<=nlstate;j++)          big=dum; 
       for(theta=1; theta <=npar; theta++)          imax=i; 
         trgradg[j][theta]=gradg[theta][j];        } 
       } 
     for(i=1;i<=nlstate;i++)      if (j != imax) { 
       varpl[i][(int)age] =0.;        for (k=1;k<=n;k++) { 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          dum=a[imax][k]; 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          a[imax][k]=a[j][k]; 
     for(i=1;i<=nlstate;i++)          a[j][k]=dum; 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        } 
         *d = -(*d); 
     fprintf(ficresvpl,"%.0f ",age );        vv[imax]=vv[j]; 
     for(i=1; i<=nlstate;i++)      } 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      indx[j]=imax; 
     fprintf(ficresvpl,"\n");      if (a[j][j] == 0.0) a[j][j]=TINY; 
     free_vector(gp,1,nlstate);      if (j != n) { 
     free_vector(gm,1,nlstate);        dum=1.0/(a[j][j]); 
     free_matrix(gradg,1,npar,1,nlstate);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     free_matrix(trgradg,1,nlstate,1,npar);      } 
   } /* End age */    } 
     free_vector(vv,1,n);  /* Doesn't work */
   free_vector(xp,1,npar);  ;
   free_matrix(doldm,1,nlstate,1,npar);  } 
   free_matrix(dnewm,1,nlstate,1,nlstate);  
   void lubksb(double **a, int n, int *indx, double b[]) 
 }  { 
     int i,ii=0,ip,j; 
 /************ Variance of one-step probabilities  ******************/    double sum; 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)   
 {    for (i=1;i<=n;i++) { 
   int i, j;      ip=indx[i]; 
   int k=0, cptcode;      sum=b[ip]; 
   double **dnewm,**doldm;      b[ip]=b[i]; 
   double *xp;      if (ii) 
   double *gp, *gm;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   double **gradg, **trgradg;      else if (sum) ii=i; 
   double age,agelim, cov[NCOVMAX];      b[i]=sum; 
   int theta;    } 
   char fileresprob[FILENAMELENGTH];    for (i=n;i>=1;i--) { 
       sum=b[i]; 
   strcpy(fileresprob,"prob");      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   strcat(fileresprob,fileres);      b[i]=sum/a[i][i]; 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    } 
     printf("Problem with resultfile: %s\n", fileresprob);  } 
   }  
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);  /************ 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)
   {  /* Some frequencies */
   xp=vector(1,npar);    
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    int first;
      double ***freq; /* Frequencies */
   cov[1]=1;    double *pp, **prop;
   for (age=bage; age<=fage; age ++){    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     cov[2]=age;    FILE *ficresp;
     gradg=matrix(1,npar,1,9);    char fileresp[FILENAMELENGTH];
     trgradg=matrix(1,9,1,npar);    
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    pp=vector(1,nlstate);
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    prop=matrix(1,nlstate,iagemin,iagemax+3);
        strcpy(fileresp,"p");
     for(theta=1; theta <=npar; theta++){    strcat(fileresp,fileres);
       for(i=1; i<=npar; i++)    if((ficresp=fopen(fileresp,"w"))==NULL) {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      printf("Problem with prevalence resultfile: %s\n", fileresp);
            fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      exit(0);
        }
       k=0;    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
       for(i=1; i<= (nlstate+ndeath); i++){    j1=0;
         for(j=1; j<=(nlstate+ndeath);j++){    
            k=k+1;    j=cptcoveff;
           gp[k]=pmmij[i][j];    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         }  
       }    first=1;
   
       for(i=1; i<=npar; i++)    for(k1=1; k1<=j;k1++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for(i1=1; i1<=ncodemax[k1];i1++){
            j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);          scanf("%d", i);*/
       k=0;        for (i=-1; i<=nlstate+ndeath; i++)  
       for(i=1; i<=(nlstate+ndeath); i++){          for (jk=-1; jk<=nlstate+ndeath; jk++)  
         for(j=1; j<=(nlstate+ndeath);j++){            for(m=iagemin; m <= iagemax+3; m++)
           k=k+1;              freq[i][jk][m]=0;
           gm[k]=pmmij[i][j];  
         }      for (i=1; i<=nlstate; i++)  
       }        for(m=iagemin; m <= iagemax+3; m++)
                prop[i][m]=0;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          dateintsum=0;
     }        k2cpt=0;
         for (i=1; i<=imx; i++) {
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          bool=1;
       for(theta=1; theta <=npar; theta++)          if  (cptcovn>0) {
       trgradg[j][theta]=gradg[theta][j];            for (z1=1; z1<=cptcoveff; z1++) 
                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);                bool=0;
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          }
           if (bool==1){
      pmij(pmmij,cov,ncovmodel,x,nlstate);            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
      k=0;              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
      for(i=1; i<=(nlstate+ndeath); i++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
        for(j=1; j<=(nlstate+ndeath);j++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
          k=k+1;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
          gm[k]=pmmij[i][j];                if (m<lastpass) {
         }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
      }                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                      }
      /*printf("\n%d ",(int)age);                
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                          dateintsum=dateintsum+k2;
                   k2cpt++;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));                }
      }*/                /*}*/
             }
   fprintf(ficresprob,"\n%d ",(int)age);          }
         }
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){         
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  
   }        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          fprintf(ficresp, "**********\n#");
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        }
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        for(i=1; i<=nlstate;i++) 
 }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
  free_vector(xp,1,npar);        fprintf(ficresp, "\n");
 fclose(ficresprob);        
  exit(0);        for(i=iagemin; i <= iagemax+3; i++){
 }          if(i==iagemax+3){
             fprintf(ficlog,"Total");
 /***********************************************/          }else{
 /**************** Main Program *****************/            if(first==1){
 /***********************************************/              first=0;
               printf("See log file for details...\n");
 int main(int argc, char *argv[])            }
 {            fprintf(ficlog,"Age %d", i);
           }
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;          for(jk=1; jk <=nlstate ; jk++){
   double agedeb, agefin,hf;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   double agemin=1.e20, agemax=-1.e20;              pp[jk] += freq[jk][m][i]; 
           }
   double fret;          for(jk=1; jk <=nlstate ; jk++){
   double **xi,tmp,delta;            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
   double dum; /* Dummy variable */            if(pp[jk]>=1.e-10){
   double ***p3mat;              if(first==1){
   int *indx;              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   char line[MAXLINE], linepar[MAXLINE];              }
   char title[MAXLINE];              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];            }else{
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];              if(first==1)
                  printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
   char filerest[FILENAMELENGTH];          }
   char fileregp[FILENAMELENGTH];  
   char popfile[FILENAMELENGTH];          for(jk=1; jk <=nlstate ; jk++){
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   int firstobs=1, lastobs=10;              pp[jk] += freq[jk][m][i];
   int sdeb, sfin; /* Status at beginning and end */          }       
   int c,  h , cpt,l;          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   int ju,jl, mi;            pos += pp[jk];
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            posprop += prop[jk][i];
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          }
   int mobilav=0,popforecast=0;          for(jk=1; jk <=nlstate ; jk++){
   int hstepm, nhstepm;            if(pos>=1.e-5){
   int *popage;/*boolprev=0 if date and zero if wave*/              if(first==1)
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   double bage, fage, age, agelim, agebase;            }else{
   double ftolpl=FTOL;              if(first==1)
   double **prlim;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   double *severity;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   double ***param; /* Matrix of parameters */            }
   double  *p;            if( i <= iagemax){
   double **matcov; /* Matrix of covariance */              if(pos>=1.e-5){
   double ***delti3; /* Scale */                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   double *delti; /* Scale */                /*probs[i][jk][j1]= pp[jk]/pos;*/
   double ***eij, ***vareij;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   double **varpl; /* Variances of prevalence limits by age */              }
   double *epj, vepp;              else
   double kk1, kk2;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   double *popeffectif,*popcount;            }
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;          }
   double yp,yp1,yp2;          
           for(jk=-1; jk <=nlstate+ndeath; jk++)
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";            for(m=-1; m <=nlstate+ndeath; m++)
   char *alph[]={"a","a","b","c","d","e"}, str[4];              if(freq[jk][m][i] !=0 ) {
               if(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   char z[1]="c", occ;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
 #include <sys/time.h>              }
 #include <time.h>          if(i <= iagemax)
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];            fprintf(ficresp,"\n");
            if(first==1)
   /* long total_usecs;            printf("Others in log...\n");
   struct timeval start_time, end_time;          fprintf(ficlog,"\n");
          }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      }
     }
     dateintmean=dateintsum/k2cpt; 
   printf("\n%s",version);   
   if(argc <=1){    fclose(ficresp);
     printf("\nEnter the parameter file name: ");    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     scanf("%s",pathtot);    free_vector(pp,1,nlstate);
   }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   else{    /* End of Freq */
     strcpy(pathtot,argv[1]);  }
   }  
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/  /************ Prevalence ********************/
   /*cygwin_split_path(pathtot,path,optionfile);  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)
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  {  
   /* cutv(path,optionfile,pathtot,'\\');*/    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);       We still use firstpass and lastpass as another selection.
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    */
   chdir(path);   
   replace(pathc,path);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     double ***freq; /* Frequencies */
 /*-------- arguments in the command line --------*/    double *pp, **prop;
     double pos,posprop; 
   strcpy(fileres,"r");    double  y2; /* in fractional years */
   strcat(fileres, optionfilefiname);    int iagemin, iagemax;
   strcat(fileres,".txt");    /* Other files have txt extension */  
     iagemin= (int) agemin;
   /*---------arguments file --------*/    iagemax= (int) agemax;
     /*pp=vector(1,nlstate);*/
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     printf("Problem with optionfile %s\n",optionfile);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     goto end;    j1=0;
   }    
     j=cptcoveff;
   strcpy(filereso,"o");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   strcat(filereso,fileres);    
   if((ficparo=fopen(filereso,"w"))==NULL) {    for(k1=1; k1<=j;k1++){
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      for(i1=1; i1<=ncodemax[k1];i1++){
   }        j1++;
         
   /* Reads comments: lines beginning with '#' */        for (i=1; i<=nlstate; i++)  
   while((c=getc(ficpar))=='#' && c!= EOF){          for(m=iagemin; m <= iagemax+3; m++)
     ungetc(c,ficpar);            prop[i][m]=0.0;
     fgets(line, MAXLINE, ficpar);       
     puts(line);        for (i=1; i<=imx; i++) { /* Each individual */
     fputs(line,ficparo);          bool=1;
   }          if  (cptcovn>0) {
   ungetc(c,ficpar);            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   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);                bool=0;
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);          } 
   fprintf(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 (bool==1) { 
 while((c=getc(ficpar))=='#' && c!= EOF){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     ungetc(c,ficpar);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     fgets(line, MAXLINE, ficpar);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     puts(line);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fputs(line,ficparo);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   ungetc(c,ficpar);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                    /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                      prop[s[m][i]][(int)agev[m][i]] += weight[i];
   covar=matrix(0,NCOVMAX,1,n);                  prop[s[m][i]][iagemax+3] += weight[i]; 
   cptcovn=0;                } 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;              }
             } /* end selection of waves */
   ncovmodel=2+cptcovn;          }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        }
          for(i=iagemin; i <= iagemax+3; i++){  
   /* Read guess parameters */          
   /* Reads comments: lines beginning with '#' */          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   while((c=getc(ficpar))=='#' && c!= EOF){            posprop += prop[jk][i]; 
     ungetc(c,ficpar);          } 
     fgets(line, MAXLINE, ficpar);  
     puts(line);          for(jk=1; jk <=nlstate ; jk++){     
     fputs(line,ficparo);            if( i <=  iagemax){ 
   }              if(posprop>=1.e-5){ 
   ungetc(c,ficpar);                probs[i][jk][j1]= prop[jk][i]/posprop;
                } 
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            } 
     for(i=1; i <=nlstate; i++)          }/* end jk */ 
     for(j=1; j <=nlstate+ndeath-1; j++){        }/* end i */ 
       fscanf(ficpar,"%1d%1d",&i1,&j1);      } /* end i1 */
       fprintf(ficparo,"%1d%1d",i1,j1);    } /* end k1 */
       printf("%1d%1d",i,j);    
       for(k=1; k<=ncovmodel;k++){    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
         fscanf(ficpar," %lf",&param[i][j][k]);    /*free_vector(pp,1,nlstate);*/
         printf(" %lf",param[i][j][k]);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
         fprintf(ficparo," %lf",param[i][j][k]);  }  /* End of prevalence */
       }  
       fscanf(ficpar,"\n");  /************* Waves Concatenation ***************/
       printf("\n");  
       fprintf(ficparo,"\n");  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)
     }  {
      /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;       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
   p=param[1][1];       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         and mw[mi+1][i]. dh depends on stepm.
   /* Reads comments: lines beginning with '#' */       */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    int i, mi, m;
     fgets(line, MAXLINE, ficpar);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     puts(line);       double sum=0., jmean=0.;*/
     fputs(line,ficparo);    int first;
   }    int j, k=0,jk, ju, jl;
   ungetc(c,ficpar);    double sum=0.;
     first=0;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    jmin=1e+5;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    jmax=-1;
   for(i=1; i <=nlstate; i++){    jmean=0.;
     for(j=1; j <=nlstate+ndeath-1; j++){    for(i=1; i<=imx; i++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);      mi=0;
       printf("%1d%1d",i,j);      m=firstpass;
       fprintf(ficparo,"%1d%1d",i1,j1);      while(s[m][i] <= nlstate){
       for(k=1; k<=ncovmodel;k++){        if(s[m][i]>=1)
         fscanf(ficpar,"%le",&delti3[i][j][k]);          mw[++mi][i]=m;
         printf(" %le",delti3[i][j][k]);        if(m >=lastpass)
         fprintf(ficparo," %le",delti3[i][j][k]);          break;
       }        else
       fscanf(ficpar,"\n");          m++;
       printf("\n");      }/* end while */
       fprintf(ficparo,"\n");      if (s[m][i] > nlstate){
     }        mi++;     /* Death is another wave */
   }        /* if(mi==0)  never been interviewed correctly before death */
   delti=delti3[1][1];           /* Only death is a correct wave */
          mw[mi][i]=m;
   /* Reads comments: lines beginning with '#' */      }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      wav[i]=mi;
     fgets(line, MAXLINE, ficpar);      if(mi==0){
     puts(line);        nbwarn++;
     fputs(line,ficparo);        if(first==0){
   }          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   ungetc(c,ficpar);          first=1;
          }
   matcov=matrix(1,npar,1,npar);        if(first==1){
   for(i=1; i <=npar; i++){          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
     fscanf(ficpar,"%s",&str);        }
     printf("%s",str);      } /* end mi==0 */
     fprintf(ficparo,"%s",str);    } /* End individuals */
     for(j=1; j <=i; j++){  
       fscanf(ficpar," %le",&matcov[i][j]);    for(i=1; i<=imx; i++){
       printf(" %.5le",matcov[i][j]);      for(mi=1; mi<wav[i];mi++){
       fprintf(ficparo," %.5le",matcov[i][j]);        if (stepm <=0)
     }          dh[mi][i]=1;
     fscanf(ficpar,"\n");        else{
     printf("\n");          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     fprintf(ficparo,"\n");            if (agedc[i] < 2*AGESUP) {
   }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   for(i=1; i <=npar; i++)              if(j==0) j=1;  /* Survives at least one month after exam */
     for(j=i+1;j<=npar;j++)              else if(j<0){
       matcov[i][j]=matcov[j][i];                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]);
   printf("\n");                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);
                 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]);
     /*-------- data file ----------*/                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);
     if((ficres =fopen(fileres,"w"))==NULL) {              }
       printf("Problem with resultfile: %s\n", fileres);goto end;              k=k+1;
     }              if (j >= jmax) jmax=j;
     fprintf(ficres,"#%s\n",version);              if (j <= jmin) jmin=j;
                  sum=sum+j;
     if((fic=fopen(datafile,"r"))==NULL)    {              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       printf("Problem with datafile: %s\n", datafile);goto end;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     }            }
           }
     n= lastobs;          else{
     severity = vector(1,maxwav);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     outcome=imatrix(1,maxwav+1,1,n);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     num=ivector(1,n);            k=k+1;
     moisnais=vector(1,n);            if (j >= jmax) jmax=j;
     annais=vector(1,n);            else if (j <= jmin)jmin=j;
     moisdc=vector(1,n);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     andc=vector(1,n);            /*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]);*/
     agedc=vector(1,n);            if(j<0){
     cod=ivector(1,n);              nberr++;
     weight=vector(1,n);              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]);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */              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]);
     mint=matrix(1,maxwav,1,n);            }
     anint=matrix(1,maxwav,1,n);            sum=sum+j;
     s=imatrix(1,maxwav+1,1,n);          }
     adl=imatrix(1,maxwav+1,1,n);              jk= j/stepm;
     tab=ivector(1,NCOVMAX);          jl= j -jk*stepm;
     ncodemax=ivector(1,8);          ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     i=1;            if(jl==0){
     while (fgets(line, MAXLINE, fic) != NULL)    {              dh[mi][i]=jk;
       if ((i >= firstobs) && (i <=lastobs)) {              bh[mi][i]=0;
                    }else{ /* We want a negative bias in order to only have interpolation ie
         for (j=maxwav;j>=1;j--){                    * at the price of an extra matrix product in likelihood */
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);              dh[mi][i]=jk+1;
           strcpy(line,stra);              bh[mi][i]=ju;
           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);          }else{
         }            if(jl <= -ju){
                      dh[mi][i]=jk;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);              bh[mi][i]=jl;       /* bias is positive if real duration
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);                                   * is higher than the multiple of stepm and negative otherwise.
                                    */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);            }
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            else{
               dh[mi][i]=jk+1;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);              bh[mi][i]=ju;
         for (j=ncov;j>=1;j--){            }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);            if(dh[mi][i]==0){
         }              dh[mi][i]=1; /* At least one step */
         num[i]=atol(stra);              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);*/
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){            }
           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;}*/          } /* end if mle */
         }
         i=i+1;      } /* end wave */
       }    }
     }    jmean=sum/k;
     /* printf("ii=%d", ij);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
        scanf("%d",i);*/    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   imx=i-1; /* Number of individuals */   }
   
   /* for (i=1; i<=imx; i++){  /*********** Tricode ****************************/
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;  void tricode(int *Tvar, int **nbcode, int imx)
     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;    
     }    int Ndum[20],ij=1, k, j, i, maxncov=19;
     int cptcode=0;
     for (i=1; i<=imx; i++)    cptcoveff=0; 
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/   
     for (k=0; k<maxncov; k++) Ndum[k]=0;
   /* Calculation of the number of parameter from char model*/    for (k=1; k<=7; k++) ncodemax[k]=0;
   Tvar=ivector(1,15);  
   Tprod=ivector(1,15);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   Tvaraff=ivector(1,15);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   Tvard=imatrix(1,15,1,2);                                 modality*/ 
   Tage=ivector(1,15);              ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
            Ndum[ij]++; /*store the modality */
   if (strlen(model) >1){        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     j=0, j1=0, k1=1, k2=1;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     j=nbocc(model,'+');                                         Tvar[j]. If V=sex and male is 0 and 
     j1=nbocc(model,'*');                                         female is 1, then  cptcode=1.*/
     cptcovn=j+1;      }
     cptcovprod=j1;  
          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 */
     strcpy(modelsav,model);      }
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  
       printf("Error. Non available option model=%s ",model);      ij=1; 
       goto end;      for (i=1; i<=ncodemax[j]; i++) {
     }        for (k=0; k<= maxncov; k++) {
              if (Ndum[k] != 0) {
     for(i=(j+1); i>=1;i--){            nbcode[Tvar[j]][ij]=k; 
       cutv(stra,strb,modelsav,'+');            /* 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; */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);            
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/            ij++;
       /*scanf("%d",i);*/          }
       if (strchr(strb,'*')) {          if (ij > ncodemax[j]) break; 
         cutv(strd,strc,strb,'*');        }  
         if (strcmp(strc,"age")==0) {      } 
           cptcovprod--;    }  
           cutv(strb,stre,strd,'V');  
           Tvar[i]=atoi(stre);   for (k=0; k< maxncov; k++) Ndum[k]=0;
           cptcovage++;  
             Tage[cptcovage]=i;   for (i=1; i<=ncovmodel-2; i++) { 
             /*printf("stre=%s ", stre);*/     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
         }     ij=Tvar[i];
         else if (strcmp(strd,"age")==0) {     Ndum[ij]++;
           cptcovprod--;   }
           cutv(strb,stre,strc,'V');  
           Tvar[i]=atoi(stre);   ij=1;
           cptcovage++;   for (i=1; i<= maxncov; i++) {
           Tage[cptcovage]=i;     if((Ndum[i]!=0) && (i<=ncovcol)){
         }       Tvaraff[ij]=i; /*For printing */
         else {       ij++;
           cutv(strb,stre,strc,'V');     }
           Tvar[i]=ncov+k1;   }
           cutv(strb,strc,strd,'V');   
           Tprod[k1]=i;   cptcoveff=ij-1; /*Number of simple covariates*/
           Tvard[k1][1]=atoi(strc);  }
           Tvard[k1][2]=atoi(stre);  
           Tvar[cptcovn+k2]=Tvard[k1][1];  /*********** Health Expectancies ****************/
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  
           for (k=1; k<=lastobs;k++)  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 )
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  
           k1++;  {
           k2=k2+2;    /* Health expectancies */
         }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
       }    double age, agelim, hf;
       else {    double ***p3mat,***varhe;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    double **dnewm,**doldm;
        /*  scanf("%d",i);*/    double *xp;
       cutv(strd,strc,strb,'V');    double **gp, **gm;
       Tvar[i]=atoi(strc);    double ***gradg, ***trgradg;
       }    int theta;
       strcpy(modelsav,stra);    
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
         scanf("%d",i);*/    xp=vector(1,npar);
     }    dnewm=matrix(1,nlstate*nlstate,1,npar);
 }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
      
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    fprintf(ficreseij,"# Health expectancies\n");
   printf("cptcovprod=%d ", cptcovprod);    fprintf(ficreseij,"# Age");
   scanf("%d ",i);*/    for(i=1; i<=nlstate;i++)
     fclose(fic);      for(j=1; j<=nlstate;j++)
         fprintf(ficreseij," %1d-%1d (SE)",i,j);
     /*  if(mle==1){*/    fprintf(ficreseij,"\n");
     if (weightopt != 1) { /* Maximisation without weights*/  
       for(i=1;i<=n;i++) weight[i]=1.0;    if(estepm < stepm){
     }      printf ("Problem %d lower than %d\n",estepm, stepm);
     /*-calculation of age at interview from date of interview and age at death -*/    }
     agev=matrix(1,maxwav,1,imx);    else  hstepm=estepm;   
     /* We compute the life expectancy from trapezoids spaced every estepm months
    for (i=1; i<=imx; i++)     * This is mainly to measure the difference between two models: for example
      for(m=2; (m<= maxwav); m++)     * if stepm=24 months pijx are given only every 2 years and by summing them
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){     * we are calculating an estimate of the Life Expectancy assuming a linear 
          anint[m][i]=9999;     * progression in between and thus overestimating or underestimating according
          s[m][i]=-1;     * to the curvature of the survival function. If, for the same date, we 
        }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         * to compare the new estimate of Life expectancy with the same linear 
     for (i=1; i<=imx; i++)  {     * hypothesis. A more precise result, taking into account a more precise
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);     * curvature will be obtained if estepm is as small as stepm. */
       for(m=1; (m<= maxwav); m++){  
         if(s[m][i] >0){    /* For example we decided to compute the life expectancy with the smallest unit */
           if (s[m][i] == nlstate+1) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
             if(agedc[i]>0)       nhstepm is the number of hstepm from age to agelim 
               if(moisdc[i]!=99 && andc[i]!=9999)       nstepm is the number of stepm from age to agelin. 
               agev[m][i]=agedc[i];       Look at hpijx to understand the reason of that which relies in memory size
             else {       and note for a fixed period like estepm months */
               if (andc[i]!=9999){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
               printf("Warning negative age at death: %d line:%d\n",num[i],i);       survival function given by stepm (the optimization length). Unfortunately it
               agev[m][i]=-1;       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.
           }    */
           else if(s[m][i] !=9){ /* Should no more exist */    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  
             if(mint[m][i]==99 || anint[m][i]==9999)    agelim=AGESUP;
               agev[m][i]=1;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
             else if(agev[m][i] <agemin){      /* nhstepm age range expressed in number of stepm */
               agemin=agev[m][i];      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
             }      /* if (stepm >= YEARM) hstepm=1;*/
             else if(agev[m][i] >agemax){      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
               agemax=agev[m][i];      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
             }      gp=matrix(0,nhstepm,1,nlstate*nlstate);
             /*agev[m][i]=anint[m][i]-annais[i];*/      gm=matrix(0,nhstepm,1,nlstate*nlstate);
             /*   agev[m][i] = age[i]+2*m;*/  
           }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
           else { /* =9 */         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
             agev[m][i]=1;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
             s[m][i]=-1;   
           }  
         }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         else /*= 0 Unknown */  
           agev[m][i]=1;      /* Computing  Variances of health expectancies */
       }  
           for(theta=1; theta <=npar; theta++){
     }        for(i=1; i<=npar; i++){ 
     for (i=1; i<=imx; i++)  {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       for(m=1; (m<= maxwav); m++){        }
         if (s[m][i] > (nlstate+ndeath)) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           printf("Error: Wrong value in nlstate or ndeath\n");      
           goto end;        cptj=0;
         }        for(j=1; j<= nlstate; j++){
       }          for(i=1; i<=nlstate; i++){
     }            cptj=cptj+1;
             for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
     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);        for(i=1; i<=npar; i++) 
        free_matrix(anint,1,maxwav,1,n);*/          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     free_vector(moisdc,1,n);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     free_vector(andc,1,n);        
         cptj=0;
            for(j=1; j<= nlstate; j++){
     wav=ivector(1,imx);          for(i=1;i<=nlstate;i++){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            cptj=cptj+1;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
      
     /* Concatenates waves */              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);            }
           }
         }
       Tcode=ivector(1,100);        for(j=1; j<= nlstate*nlstate; j++)
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          for(h=0; h<=nhstepm-1; h++){
       ncodemax[1]=1;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          }
             } 
    codtab=imatrix(1,100,1,10);     
    h=0;  /* End theta */
    m=pow(2,cptcoveff);  
         trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){       for(h=0; h<=nhstepm-1; h++)
        for(j=1; j <= ncodemax[k]; j++){        for(j=1; j<=nlstate*nlstate;j++)
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          for(theta=1; theta <=npar; theta++)
            h++;            trgradg[h][j][theta]=gradg[h][theta][j];
            if (h>m) h=1;codtab[h][k]=j;       
          }  
        }       for(i=1;i<=nlstate*nlstate;i++)
      }        for(j=1;j<=nlstate*nlstate;j++)
    }          varhe[i][j][(int)age] =0.;
   
        printf("%d|",(int)age);fflush(stdout);
    /*for(i=1; i <=m ;i++){       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
      for(k=1; k <=cptcovn; k++){       for(h=0;h<=nhstepm-1;h++){
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);        for(k=0;k<=nhstepm-1;k++){
      }          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
      printf("\n");          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
    }          for(i=1;i<=nlstate*nlstate;i++)
    scanf("%d",i);*/            for(j=1;j<=nlstate*nlstate;j++)
                  varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
    /* Calculates basic frequencies. Computes observed prevalence at single age        }
        and prints on file fileres'p'. */      }
       /* Computing expectancies */
          for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate;j++)
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /* 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]);*/
     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] */      fprintf(ficreseij,"%3.0f",age );
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      cptj=0;
       for(i=1; i<=nlstate;i++)
     if(mle==1){        for(j=1; j<=nlstate;j++){
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          cptj++;
     }          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
            }
     /*--------- results files --------------*/      fprintf(ficreseij,"\n");
     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);     
        free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
    jk=1;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
    fprintf(ficres,"# Parameters\n");      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
    printf("# Parameters\n");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    for(i=1,jk=1; i <=nlstate; i++){    }
      for(k=1; k <=(nlstate+ndeath); k++){    printf("\n");
        if (k != i)    fprintf(ficlog,"\n");
          {  
            printf("%d%d ",i,k);    free_vector(xp,1,npar);
            fprintf(ficres,"%1d%1d ",i,k);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
            for(j=1; j <=ncovmodel; j++){    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
              printf("%f ",p[jk]);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
              fprintf(ficres,"%f ",p[jk]);  }
              jk++;  
            }  /************ Variance ******************/
            printf("\n");  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
            fprintf(ficres,"\n");  {
          }    /* Variance of health expectancies */
      }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
    }    /* double **newm;*/
  if(mle==1){    double **dnewm,**doldm;
     /* Computing hessian and covariance matrix */    double **dnewmp,**doldmp;
     ftolhess=ftol; /* Usually correct */    int i, j, nhstepm, hstepm, h, nstepm ;
     hesscov(matcov, p, npar, delti, ftolhess, func);    int k, cptcode;
  }    double *xp;
     fprintf(ficres,"# Scales\n");    double **gp, **gm;  /* for var eij */
     printf("# Scales\n");    double ***gradg, ***trgradg; /*for var eij */
      for(i=1,jk=1; i <=nlstate; i++){    double **gradgp, **trgradgp; /* for var p point j */
       for(j=1; j <=nlstate+ndeath; j++){    double *gpp, *gmp; /* for var p point j */
         if (j!=i) {    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
           fprintf(ficres,"%1d%1d",i,j);    double ***p3mat;
           printf("%1d%1d",i,j);    double age,agelim, hf;
           for(k=1; k<=ncovmodel;k++){    double ***mobaverage;
             printf(" %.5e",delti[jk]);    int theta;
             fprintf(ficres," %.5e",delti[jk]);    char digit[4];
             jk++;    char digitp[25];
           }  
           printf("\n");    char fileresprobmorprev[FILENAMELENGTH];
           fprintf(ficres,"\n");  
         }    if(popbased==1){
       }      if(mobilav!=0)
      }        strcpy(digitp,"-populbased-mobilav-");
          else strcpy(digitp,"-populbased-nomobil-");
     k=1;    }
     fprintf(ficres,"# Covariance\n");    else 
     printf("# Covariance\n");      strcpy(digitp,"-stablbased-");
     for(i=1;i<=npar;i++){  
       /*  if (k>nlstate) k=1;    if (mobilav!=0) {
       i1=(i-1)/(ncovmodel*nlstate)+1;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       printf("%s%d%d",alph[k],i1,tab[i]);*/        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       fprintf(ficres,"%3d",i);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       printf("%3d",i);      }
       for(j=1; j<=i;j++){    }
         fprintf(ficres," %.5e",matcov[i][j]);  
         printf(" %.5e",matcov[i][j]);    strcpy(fileresprobmorprev,"prmorprev"); 
       }    sprintf(digit,"%-d",ij);
       fprintf(ficres,"\n");    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       printf("\n");    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       k++;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     }    strcat(fileresprobmorprev,fileres);
        if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     while((c=getc(ficpar))=='#' && c!= EOF){      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       ungetc(c,ficpar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       fgets(line, MAXLINE, ficpar);    }
       puts(line);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       fputs(line,ficparo);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     }    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);
     ungetc(c,ficpar);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      fprintf(ficresprobmorprev," p.%-d SE",j);
          for(i=1; i<=nlstate;i++)
     if (fage <= 2) {        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
       bage = agemin;    }  
       fage = agemax;    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");
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     fprintf(ficres,"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);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    
     while((c=getc(ficpar))=='#' && c!= EOF){    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");
     ungetc(c,ficpar);    fprintf(ficresvij,"# Age");
     fgets(line, MAXLINE, ficpar);    for(i=1; i<=nlstate;i++)
     puts(line);      for(j=1; j<=nlstate;j++)
     fputs(line,ficparo);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   }    fprintf(ficresvij,"\n");
   ungetc(c,ficpar);  
      xp=vector(1,npar);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);    dnewm=matrix(1,nlstate,1,npar);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);    doldm=matrix(1,nlstate,1,nlstate);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
          doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     fgets(line, MAXLINE, ficpar);    gpp=vector(nlstate+1,nlstate+ndeath);
     puts(line);    gmp=vector(nlstate+1,nlstate+ndeath);
     fputs(line,ficparo);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   }    
   ungetc(c,ficpar);    if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
     }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    else  hstepm=estepm;   
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    /* 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. 
   fscanf(ficpar,"pop_based=%d\n",&popbased);       nhstepm is the number of hstepm from age to agelim 
    fprintf(ficparo,"pop_based=%d\n",popbased);         nstepm is the number of stepm from age to agelin. 
    fprintf(ficres,"pop_based=%d\n",popbased);         Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
   while((c=getc(ficpar))=='#' && c!= EOF){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     ungetc(c,ficpar);       survival function given by stepm (the optimization length). Unfortunately it
     fgets(line, MAXLINE, ficpar);       means that if the survival funtion is printed every two years of age and if
     puts(line);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     fputs(line,ficparo);       results. So we changed our mind and took the option of the best precision.
   }    */
   ungetc(c,ficpar);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);    agelim = AGESUP;
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);      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 */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
          gp=matrix(0,nhstepm,1,nlstate);
     /*------------ gnuplot -------------*/      gm=matrix(0,nhstepm,1,nlstate);
     /*chdir(pathcd);*/  
     strcpy(optionfilegnuplot,optionfilefiname);  
     strcat(optionfilegnuplot,".plt");      for(theta=1; theta <=npar; theta++){
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       printf("Problem with file %s",optionfilegnuplot);goto end;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     }        }
 #ifdef windows        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fprintf(ficgp,"cd \"%s\" \n",pathc);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 #endif  
 m=pow(2,cptcoveff);        if (popbased==1) {
            if(mobilav ==0){
  /* 1eme*/            for(i=1; i<=nlstate;i++)
   for (cpt=1; cpt<= nlstate ; cpt ++) {              prlim[i][i]=probs[(int)age][i][ij];
    for (k1=1; k1<= m ; k1 ++) {          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
 #ifdef windows              prlim[i][i]=mobaverage[(int)age][i][ij];
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);          }
 #endif        }
 #ifdef unix    
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);        for(j=1; j<= nlstate; j++){
 #endif          for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
 for (i=1; i<= nlstate ; i ++) {              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }        /* This for computing probability of death (h=1 means
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);           computed over hstepm matrices product = hstepm*stepm months) 
     for (i=1; i<= nlstate ; i ++) {           as a weighted average of prlim.
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        */
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
 }          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
      for (i=1; i<= nlstate ; i ++) {        }    
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        /* end probability of death */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }          for(i=1; i<=npar; i++) /* Computes gradient x - delta */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 #ifdef unix        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 fprintf(ficgp,"\nset ter gif small size 400,300");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 #endif   
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        if (popbased==1) {
    }          if(mobilav ==0){
   }            for(i=1; i<=nlstate;i++)
   /*2 eme*/              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
   for (k1=1; k1<= m ; k1 ++) {            for(i=1; i<=nlstate;i++)
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);              prlim[i][i]=mobaverage[(int)age][i][ij];
              }
     for (i=1; i<= nlstate+1 ; i ++) {        }
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        for(j=1; j<= nlstate; j++){
       for (j=1; j<= nlstate+1 ; j ++) {          for(h=0; h<=nhstepm; h++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
 }            }
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        /* This for computing probability of death (h=1 means
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);           computed over hstepm matrices product = hstepm*stepm months) 
       for (j=1; j<= nlstate+1 ; j ++) {           as a weighted average of prlim.
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        */
         else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
 }            for(i=1,gmp[j]=0.; i<= nlstate; i++)
       fprintf(ficgp,"\" t\"\" w l 0,");           gmp[j] += prlim[i][i]*p3mat[i][j][1];
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        }    
       for (j=1; j<= nlstate+1 ; j ++) {        /* end probability of death */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=1; j<= nlstate; j++) /* vareij */
 }            for(h=0; h<=nhstepm; h++){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       else fprintf(ficgp,"\" t\"\" w l 0,");          }
     }  
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   }          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
          }
   /*3eme*/  
       } /* End theta */
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<= nlstate ; cpt ++) {      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       k=2+nlstate*(cpt-1);  
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);      for(h=0; h<=nhstepm; h++) /* veij */
       for (i=1; i< nlstate ; i ++) {        for(j=1; j<=nlstate;j++)
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);          for(theta=1; theta <=npar; theta++)
       }            trgradg[h][j][theta]=gradg[h][theta][j];
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   }        for(theta=1; theta <=npar; theta++)
            trgradgp[j][theta]=gradgp[theta][j];
   /* CV preval stat */    
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<nlstate ; cpt ++) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       k=3;      for(i=1;i<=nlstate;i++)
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);        for(j=1;j<=nlstate;j++)
       for (i=1; i< nlstate ; i ++)          vareij[i][j][(int)age] =0.;
         fprintf(ficgp,"+$%d",k+i+1);  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      for(h=0;h<=nhstepm;h++){
              for(k=0;k<=nhstepm;k++){
       l=3+(nlstate+ndeath)*cpt;          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       for (i=1; i< nlstate ; i ++) {          for(i=1;i<=nlstate;i++)
         l=3+(nlstate+ndeath)*cpt;            for(j=1;j<=nlstate;j++)
         fprintf(ficgp,"+$%d",l+i+1);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       }        }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        }
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    
     }      /* pptj */
   }        matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   /* proba elementaires */      for(j=nlstate+1;j<=nlstate+ndeath;j++)
    for(i=1,jk=1; i <=nlstate; i++){        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     for(k=1; k <=(nlstate+ndeath); k++){          varppt[j][i]=doldmp[j][i];
       if (k != i) {      /* end ppptj */
         for(j=1; j <=ncovmodel; j++){      /*  x centered again */
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
           /*fprintf(ficgp,"%s",alph[1]);*/      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);   
           jk++;      if (popbased==1) {
           fprintf(ficgp,"\n");        if(mobilav ==0){
         }          for(i=1; i<=nlstate;i++)
       }            prlim[i][i]=probs[(int)age][i][ij];
     }        }else{ /* mobilav */ 
     }          for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
   for(jk=1; jk <=m; jk++) {        }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);      }
    i=1;               
    for(k2=1; k2<=nlstate; k2++) {      /* This for computing probability of death (h=1 means
      k3=i;         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
      for(k=1; k<=(nlstate+ndeath); k++) {         as a weighted average of prlim.
        if (k != k2){      */
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
 ij=1;        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
         for(j=3; j <=ncovmodel; j++) {          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           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]]]);      /* end probability of death */
             ij++;  
           }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
           else      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         }        for(i=1; i<=nlstate;i++){
           fprintf(ficgp,")/(1");          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
                }
         for(k1=1; k1 <=nlstate; k1++){        } 
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      fprintf(ficresprobmorprev,"\n");
 ij=1;  
           for(j=3; j <=ncovmodel; j++){      fprintf(ficresvij,"%.0f ",age );
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      for(i=1; i<=nlstate;i++)
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        for(j=1; j<=nlstate;j++){
             ij++;          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
           }        }
           else      fprintf(ficresvij,"\n");
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      free_matrix(gp,0,nhstepm,1,nlstate);
           }      free_matrix(gm,0,nhstepm,1,nlstate);
           fprintf(ficgp,")");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
         }      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    } /* End age */
         i=i+ncovmodel;    free_vector(gpp,nlstate+1,nlstate+ndeath);
        }    free_vector(gmp,nlstate+1,nlstate+ndeath);
      }    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
    }    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   }    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
        fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   fclose(ficgp);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /* end gnuplot */  /*   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); */
 chdir(path);    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));
     free_ivector(wav,1,imx);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      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);
     free_ivector(num,1,n);    /*  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);
     free_vector(agedc,1,n);  */
     /*free_matrix(covar,1,NCOVMAX,1,n);*/  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fclose(ficparo);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     fclose(ficres);  
     /*  }*/    free_vector(xp,1,npar);
        free_matrix(doldm,1,nlstate,1,nlstate);
    /*________fin mle=1_________*/    free_matrix(dnewm,1,nlstate,1,npar);
        free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
      free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     /* No more information from the sample is required now */    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   /* Reads comments: lines beginning with '#' */    fclose(ficresprobmorprev);
   while((c=getc(ficpar))=='#' && c!= EOF){    fflush(ficgp);
     ungetc(c,ficpar);    fflush(fichtm); 
     fgets(line, MAXLINE, ficpar);  }  /* end varevsij */
     puts(line);  
     fputs(line,ficparo);  /************ Variance of prevlim ******************/
   }  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
   ungetc(c,ficpar);  {
      /* Variance of prevalence limit */
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);    double **newm;
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    double **dnewm,**doldm;
 /*--------- index.htm --------*/    int i, j, nhstepm, hstepm;
     int k, cptcode;
   strcpy(optionfilehtm,optionfile);    double *xp;
   strcat(optionfilehtm,".htm");    double *gp, *gm;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    double **gradg, **trgradg;
     printf("Problem with %s \n",optionfilehtm);goto end;    double age,agelim;
   }    int theta;
      
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    fprintf(ficresvpl,"# Age");
 Total number of observations=%d <br>    for(i=1; i<=nlstate;i++)
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>        fprintf(ficresvpl," %1d-%1d",i,i);
 <hr  size=\"2\" color=\"#EC5E5E\">    fprintf(ficresvpl,"\n");
 <li>Outputs files<br><br>\n  
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    xp=vector(1,npar);
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    dnewm=matrix(1,nlstate,1,npar);
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    doldm=matrix(1,nlstate,1,nlstate);
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    hstepm=1*YEARM; /* Every year of age */
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    agelim = AGESUP;
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>      if (stepm >= YEARM) hstepm=1;
 <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);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
  fprintf(fichtm," <li>Graphs</li><p>");      gp=vector(1,nlstate);
       gm=vector(1,nlstate);
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
  j1=0;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
  for(k1=1; k1<=m;k1++){        }
    for(i1=1; i1<=ncodemax[k1];i1++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        j1++;        for(i=1;i<=nlstate;i++)
        if (cptcovn > 0) {          gp[i] = prlim[i][i];
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      
          for (cpt=1; cpt<=cptcoveff;cpt++)        for(i=1; i<=npar; i++) /* Computes gradient */
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
        }        for(i=1;i<=nlstate;i++)
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          gm[i] = prlim[i][i];
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);      
        for(cpt=1; cpt<nlstate;cpt++){        for(i=1;i<=nlstate;i++)
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      } /* End theta */
        }  
     for(cpt=1; cpt<=nlstate;cpt++) {      trgradg =matrix(1,nlstate,1,npar);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  
 interval) in state (%d): v%s%d%d.gif <br>      for(j=1; j<=nlstate;j++)
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          for(theta=1; theta <=npar; theta++)
      }          trgradg[j][theta]=gradg[theta][j];
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      for(i=1;i<=nlstate;i++)
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        varpl[i][(int)age] =0.;
      }      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
 health expectancies in states (1) and (2): e%s%d.gif<br>      for(i=1;i<=nlstate;i++)
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
 fprintf(fichtm,"\n</body>");  
    }      fprintf(ficresvpl,"%.0f ",age );
  }      for(i=1; i<=nlstate;i++)
 fclose(fichtm);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
   /*--------------- Prevalence limit --------------*/      free_vector(gp,1,nlstate);
        free_vector(gm,1,nlstate);
   strcpy(filerespl,"pl");      free_matrix(gradg,1,npar,1,nlstate);
   strcat(filerespl,fileres);      free_matrix(trgradg,1,nlstate,1,npar);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    } /* End age */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  
   }    free_vector(xp,1,npar);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    free_matrix(doldm,1,nlstate,1,npar);
   fprintf(ficrespl,"#Prevalence limit\n");    free_matrix(dnewm,1,nlstate,1,nlstate);
   fprintf(ficrespl,"#Age ");  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  }
   fprintf(ficrespl,"\n");  
    /************ Variance of one-step probabilities  ******************/
   prlim=matrix(1,nlstate,1,nlstate);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  {
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int i, j=0,  i1, k1, l1, t, tj;
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int k2, l2, j1,  z1;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int k=0,l, cptcode;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    int first=1, first1;
   k=0;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   agebase=agemin;    double **dnewm,**doldm;
   agelim=agemax;    double *xp;
   ftolpl=1.e-10;    double *gp, *gm;
   i1=cptcoveff;    double **gradg, **trgradg;
   if (cptcovn < 1){i1=1;}    double **mu;
     double age,agelim, cov[NCOVMAX];
   for(cptcov=1;cptcov<=i1;cptcov++){    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int theta;
         k=k+1;    char fileresprob[FILENAMELENGTH];
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    char fileresprobcov[FILENAMELENGTH];
         fprintf(ficrespl,"\n#******");    char fileresprobcor[FILENAMELENGTH];
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double ***varpij;
         fprintf(ficrespl,"******\n");  
            strcpy(fileresprob,"prob"); 
         for (age=agebase; age<=agelim; age++){    strcat(fileresprob,fileres);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
           fprintf(ficrespl,"%.0f",age );      printf("Problem with resultfile: %s\n", fileresprob);
           for(i=1; i<=nlstate;i++)      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
           fprintf(ficrespl," %.5f", prlim[i][i]);    }
           fprintf(ficrespl,"\n");    strcpy(fileresprobcov,"probcov"); 
         }    strcat(fileresprobcov,fileres);
       }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     }      printf("Problem with resultfile: %s\n", fileresprobcov);
   fclose(ficrespl);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
   /*------------- h Pij x at various ages ------------*/    strcpy(fileresprobcor,"probcor"); 
      strcat(fileresprobcor,fileres);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      printf("Problem with resultfile: %s\n", fileresprobcor);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   }    }
   printf("Computing pij: result on file '%s' \n", filerespij);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
      fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   /*if (stepm<=24) stepsize=2;*/    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);
   agelim=AGESUP;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   hstepm=stepsize*YEARM; /* Every year of age */    
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
      fprintf(ficresprob,"# Age");
   k=0;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficresprobcov,"# Age");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
       k=k+1;    fprintf(ficresprobcov,"# Age");
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for(i=1; i<=nlstate;i++)
         fprintf(ficrespij,"******\n");      for(j=1; j<=(nlstate+ndeath);j++){
                fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        fprintf(ficresprobcov," p%1d-%1d ",i,j);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        fprintf(ficresprobcor," p%1d-%1d ",i,j);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      }  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   /* fprintf(ficresprob,"\n");
           oldm=oldms;savm=savms;    fprintf(ficresprobcov,"\n");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(ficresprobcor,"\n");
           fprintf(ficrespij,"# Age");   */
           for(i=1; i<=nlstate;i++)   xp=vector(1,npar);
             for(j=1; j<=nlstate+ndeath;j++)    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
               fprintf(ficrespij," %1d-%1d",i,j);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
           fprintf(ficrespij,"\n");    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
           for (h=0; h<=nhstepm; h++){    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    first=1;
             for(i=1; i<=nlstate;i++)    fprintf(ficgp,"\n# Routine varprob");
               for(j=1; j<=nlstate+ndeath;j++)    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    fprintf(fichtm,"\n");
             fprintf(ficrespij,"\n");  
           }    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
           fprintf(ficrespij,"\n");    file %s<br>\n",optionfilehtmcov);
         }    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
     }  and drawn. It helps understanding how is the covariance between two incidences.\
   }   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   fclose(ficrespij);  standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
   if(stepm == 1) {   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   /*---------- Forecasting ------------------*/  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  
     cov[1]=1;
   /*printf("calage= %f", calagedate);*/    tj=cptcoveff;
      if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
   strcpy(fileresf,"f");        j1++;
   strcat(fileresf,fileres);        if  (cptcovn>0) {
   if((ficresf=fopen(fileresf,"w"))==NULL) {          fprintf(ficresprob, "\n#********** Variable "); 
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   }          fprintf(ficresprob, "**********\n#\n");
   printf("Computing forecasting: result on file '%s' \n", fileresf);          fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   free_matrix(mint,1,maxwav,1,n);          fprintf(ficresprobcov, "**********\n#\n");
   free_matrix(anint,1,maxwav,1,n);          
   free_matrix(agev,1,maxwav,1,imx);          fprintf(ficgp, "\n#********** Variable "); 
   /* Mobile average */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          
           
   if (mobilav==1) {          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
       for (i=1; i<=nlstate;i++)          
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          fprintf(ficresprobcor, "\n#********** Variable ");    
           mobaverage[(int)agedeb][i][cptcod]=0.;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
              fprintf(ficresprobcor, "**********\n#");    
     for (agedeb=bage+4; agedeb<=fage; agedeb++){        }
       for (i=1; i<=nlstate;i++){        
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for (age=bage; age<=fage; age ++){ 
           for (cpt=0;cpt<=4;cpt++){          cov[2]=age;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          for (k=1; k<=cptcovn;k++) {
           }            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          }
         }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       }          for (k=1; k<=cptcovprod;k++)
     }              cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   }          
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   stepsize=(int) (stepm+YEARM-1)/YEARM;          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   if (stepm<=12) stepsize=1;          gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
   agelim=AGESUP;      
   /*hstepm=stepsize*YEARM; *//* Every year of age */          for(theta=1; theta <=npar; theta++){
   hstepm=1;            for(i=1; i<=npar; i++)
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   yp1=modf(dateintmean,&yp);            
   anprojmean=yp;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   yp2=modf((yp1*12),&yp);            
   mprojmean=yp;            k=0;
   yp1=modf((yp2*30.5),&yp);            for(i=1; i<= (nlstate); i++){
   jprojmean=yp;              for(j=1; j<=(nlstate+ndeath);j++){
   if(jprojmean==0) jprojmean=1;                k=k+1;
   if(mprojmean==0) jprojmean=1;                gp[k]=pmmij[i][j];
               }
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);            }
             
   if (popforecast==1) {            for(i=1; i<=npar; i++)
     if((ficpop=fopen(popfile,"r"))==NULL)    {              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       printf("Problem with population file : %s\n",popfile);goto end;      
     }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     popage=ivector(0,AGESUP);            k=0;
     popeffectif=vector(0,AGESUP);            for(i=1; i<=(nlstate); i++){
     popcount=vector(0,AGESUP);              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
     i=1;                  gm[k]=pmmij[i][j];
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)              }
       {            }
         i=i+1;       
       }            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     imx=i;              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
              }
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];  
   }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
   for(cptcov=1;cptcov<=i1;cptcov++){              trgradg[j][theta]=gradg[theta][j];
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          
       k=k+1;          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
       fprintf(ficresf,"\n#******");          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       for(j=1;j<=cptcoveff;j++) {          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
       }          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       fprintf(ficresf,"******\n");          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       fprintf(ficresf,"# StartingAge FinalAge");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);          pmij(pmmij,cov,ncovmodel,x,nlstate);
       if (popforecast==1)  fprintf(ficresf," [Population]");          
              k=0;
       for (cpt=0; cpt<4;cpt++) {          for(i=1; i<=(nlstate); i++){
         fprintf(ficresf,"\n");            for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);                k=k+1;
               mu[k][(int) age]=pmmij[i][j];
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */            }
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          }
         nhstepm = nhstepm/hstepm;          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         oldm=oldms;savm=savms;          /*printf("\n%d ",(int)age);
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                    printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         for (h=0; h<=nhstepm; h++){            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
           if (h==(int) (calagedate+YEARM*cpt)) {            }*/
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);  
           }          fprintf(ficresprob,"\n%d ",(int)age);
           for(j=1; j<=nlstate+ndeath;j++) {          fprintf(ficresprobcov,"\n%d ",(int)age);
             kk1=0.;kk2=0;          fprintf(ficresprobcor,"\n%d ",(int)age);
             for(i=1; i<=nlstate;i++) {          
               if (mobilav==1)          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
               else {          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
               }          }
           i=0;
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];          for (k=1; k<=(nlstate);k++){
             }            for (l=1; l<=(nlstate+ndeath);l++){ 
                        i=i++;
             if (h==(int)(calagedate+12*cpt)){              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresf," %.3f", kk1);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                            for (j=1; j<=i;j++){
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);                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]));
           }              }
         }            }
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }/* end of loop for state */
       }        } /* end of loop for age */
       }  
     }        /* Confidence intervalle of pij  */
   }        /*
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(ficgp,"\nset noparametric;unset label");
   if (popforecast==1) {          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     free_ivector(popage,0,AGESUP);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     free_vector(popeffectif,0,AGESUP);          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);
     free_vector(popcount,0,AGESUP);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   }          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   free_imatrix(s,1,maxwav+1,1,n);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   free_vector(weight,1,n);        */
   fclose(ficresf);  
   }/* End forecasting */        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   else{        first1=1;
     erreur=108;        for (k2=1; k2<=(nlstate);k2++){
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   }            if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
   /*---------- Health expectancies and variances ------------*/            for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   strcpy(filerest,"t");                if(l1==k1) continue;
   strcat(filerest,fileres);                i=(k1-1)*(nlstate+ndeath)+l1;
   if((ficrest=fopen(filerest,"w"))==NULL) {                if(i<=j) continue;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                for (age=bage; age<=fage; age ++){ 
   }                  if ((int)age %5==0){
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   strcpy(filerese,"e");                    mu1=mu[i][(int) age]/stepm*YEARM ;
   strcat(filerese,fileres);                    mu2=mu[j][(int) age]/stepm*YEARM;
   if((ficreseij=fopen(filerese,"w"))==NULL) {                    c12=cv12/sqrt(v1*v2);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); 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 Health Expectancies: result on file '%s' \n", filerese);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
  strcpy(fileresv,"v");                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   strcat(fileresv,fileres);                    /*v21=sqrt(1.-v11*v11); *//* error */
   if((ficresvij=fopen(fileresv,"w"))==NULL) {                    v21=(lc1-v1)/cv12*v11;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);                    v12=-v21;
   }                    v22=v11;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);                    tnalp=v21/v11;
                     if(first1==1){
   k=0;                      first1=0;
   for(cptcov=1;cptcov<=i1;cptcov++){                      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);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    }
       k=k+1;                    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);
       fprintf(ficrest,"\n#****** ");                    /*printf(fignu*/
       for(j=1;j<=cptcoveff;j++)                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
       fprintf(ficrest,"******\n");                    if(first==1){
                       first=0;
       fprintf(ficreseij,"\n#****** ");                      fprintf(ficgp,"\nset parametric;unset label");
       for(j=1;j<=cptcoveff;j++)                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       fprintf(ficreseij,"******\n");                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
       fprintf(ficresvij,"\n#****** ");  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
       for(j=1;j<=cptcoveff;j++)                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
       fprintf(ficresvij,"******\n");                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
       oldm=oldms;savm=savms;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);                        fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                      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",\
       oldm=oldms;savm=savms;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                          }else{
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                      first=0;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
       fprintf(ficrest,"\n");                      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);
       hf=1;                      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",\
       if (stepm >= YEARM) hf=stepm/YEARM;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       epj=vector(1,nlstate+1);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       for(age=bage; age <=fage ;age++){                    }/* if first */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                  } /* age mod 5 */
         if (popbased==1) {                } /* end loop age */
           for(i=1; i<=nlstate;i++)                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
             prlim[i][i]=probs[(int)age][i][k];                first=1;
         }              } /*l12 */
                    } /* k12 */
         fprintf(ficrest," %.0f",age);          } /*l1 */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){        }/* k1 */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      } /* loop covariates */
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    }
           }    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
           epj[nlstate+1] +=epj[j];    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
         }    free_vector(xp,1,npar);
         for(i=1, vepp=0.;i <=nlstate;i++)    fclose(ficresprob);
           for(j=1;j <=nlstate;j++)    fclose(ficresprobcov);
             vepp += vareij[i][j][(int)age];    fclose(ficresprobcor);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    fflush(ficgp);
         for(j=1;j <=nlstate;j++){    fflush(fichtmcov);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));  }
         }  
         fprintf(ficrest,"\n");  
       }  /******************* 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){
  fclose(ficreseij);    int jj1, k1, i1, cpt;
  fclose(ficresvij);    /*char optionfilehtm[FILENAMELENGTH];*/
   fclose(ficrest);  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
   fclose(ficpar);  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
   free_vector(epj,1,nlstate+1);  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
   /*  scanf("%d ",i); */  /*   } */
   
   /*------- Variance limit prevalence------*/       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 \
 strcpy(fileresvpl,"vpl");   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
   strcat(fileresvpl,fileres);   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {   - Life expectancies by age and initial health status (estepm=%2d months): \
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);     <a href=\"%s\">%s</a> <br>\n</li>", \
     exit(0);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
   }             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
  k=0;  
  for(cptcov=1;cptcov<=i1;cptcov++){  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
      k=k+1;   m=cptcoveff;
      fprintf(ficresvpl,"\n#****** ");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
      for(j=1;j<=cptcoveff;j++)  
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   jj1=0;
      fprintf(ficresvpl,"******\n");   for(k1=1; k1<=m;k1++){
           for(i1=1; i1<=ncodemax[k1];i1++){
      varpl=matrix(1,nlstate,(int) bage, (int) fage);       jj1++;
      oldm=oldms;savm=savms;       if (cptcovn > 0) {
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);         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\">");
   fclose(ficresvpl);       }
        /* Pij */
   /*---------- End : free ----------------*/       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> \
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
         /* Quasi-incidences */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);   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 */
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);         for(cpt=1; cpt<nlstate;cpt++){
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);         }
         for(cpt=1; cpt<=nlstate;cpt++) {
   free_matrix(matcov,1,npar,1,npar);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   free_vector(delti,1,npar);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
         }
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   if(erreur >0)  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
     printf("End of Imach with error %d\n",erreur);     } /* end i1 */
   else   printf("End of Imach\n");   }/* End k1 */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */   fprintf(fichtm,"</ul>");
    
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/  
   /*printf("Total time was %d uSec.\n", total_usecs);*/   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
   /*------ End -----------*/   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
    - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
  end:   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
 #ifdef windows   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
   /* chdir(pathcd);*/   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
 #endif   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
  /*system("wgnuplot graph.plt");*/           rfileres,rfileres,\
  /*system("../gp37mgw/wgnuplot graph.plt");*/           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
  /*system("cd ../gp37mgw");*/           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
  strcpy(plotcmd,GNUPLOTPROGRAM);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
  strcat(plotcmd," ");           subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
  strcat(plotcmd,optionfilegnuplot);           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
  system(plotcmd);  
   /*  if(popforecast==1) fprintf(fichtm,"\n */
 #ifdef windows  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   while (z[0] != 'q') {  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
     chdir(path);  /*      <br>",fileres,fileres,fileres,fileres); */
     printf("\nType e to edit output files, c to start again, and q for exiting: ");  /*  else  */
     scanf("%s",z);  /*    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); */
     if (z[0] == 'c') system("./imach");  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
     else if (z[0] == 'e') {  
       chdir(path);   m=cptcoveff;
       system(optionfilehtm);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     }  
     else if (z[0] == 'q') exit(0);   jj1=0;
   }   for(k1=1; k1<=m;k1++){
 #endif     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);  
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
    
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){
       j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;
         j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     }  
     fflush(ficlog);
   
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1-i)*(j1-j)!=0){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         fprintf(ficlog,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
           fprintf(ficlog," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
         fprintf(ficlog,"\n");
       }
     }
     fflush(ficlog);
   
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
         }
         fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       numlinepar++;
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
     fflush(ficlog);
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     globpr=1; /* to print the contributions */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           printf("%d%d ",i,k);
           fprintf(ficlog,"%d%d ",i,k);
           fprintf(ficres,"%1d%1d ",i,k);
           for(j=1; j <=ncovmodel; j++){
             printf("%f ",p[jk]);
             fprintf(ficlog,"%f ",p[jk]);
             fprintf(ficres,"%f ",p[jk]);
             jk++; 
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
     if(mle!=0){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle>=1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
   
   
   /* Just to have a covariance matrix which will be more understandable
      even is we still don't want to manage dictionary of variables
   */
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               if(mle>=1)
                 printf("#%1d%1d%d",i,j,k);
               fprintf(ficlog,"#%1d%1d%d",i,j,k);
               fprintf(ficres,"#%1d%1d%d",i,j,k);
             }else{
               if(mle>=1)
                 printf("%1d%1d%d",i,j,k);
               fprintf(ficlog,"%1d%1d%d",i,j,k);
               fprintf(ficres,"%1d%1d%d",i,j,k);
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         if(mle>=1)
                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         if(mle>=1)
                           printf(" %.5e",matcov[jj][ll]); 
                         fprintf(ficlog," %.5e",matcov[jj][ll]); 
                         fprintf(ficres," %.5e",matcov[jj][ll]); 
                       }
                     }else{
                       if(itimes==1){
                         if(mle>=1)
                           printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         if(mle>=1)
                           printf(" %.5e",matcov[jj][ll]); 
                         fprintf(ficlog," %.5e",matcov[jj][ll]); 
                         fprintf(ficres," %.5e",matcov[jj][ll]); 
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             if(mle>=1)
               printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
     fflush(ficlog);
     fflush(ficres);
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
     replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     /*  chdir(path); */
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_lvector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     if((outcmd=system(plotcmd)) != 0){
       printf(" Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   
Removed from v.1.22  
changed lines
  Added in v.1.95

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