Diff for /imach/src/imach.c between versions 1.49 and 1.94

version 1.49, 2002/06/20 14:03:39 version 1.94, 2003/06/27 13:00:02
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.94  2003/06/27 13:00:02  brouard
      Just cleaning
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.93  2003/06/25 16:33:55  brouard
   first survey ("cross") where individuals from different ages are    (Module): On windows (cygwin) function asctime_r doesn't
   interviewed on their health status or degree of disability (in the    exist so I changed back to asctime which exists.
   case of a health survey which is our main interest) -2- at least a    (Module): Version 0.96b
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.92  2003/06/25 16:30:45  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  
   simplest model is the multinomial logistic model where pij is the    Revision 1.91  2003/06/25 15:30:29  brouard
   probability to be observed in state j at the second wave    * imach.c (Repository): Duplicated warning errors corrected.
   conditional to be observed in state i at the first wave. Therefore    (Repository): Elapsed time after each iteration is now output. It
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    helps to forecast when convergence will be reached. Elapsed time
   'age' is age and 'sex' is a covariate. If you want to have a more    is stamped in powell.  We created a new html file for the graphs
   complex model than "constant and age", you should modify the program    concerning matrix of covariance. It has extension -cov.htm.
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Revision 1.90  2003/06/24 12:34:15  brouard
   convergence.    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
   The advantage of this computer programme, compared to a simple    of the covariance matrix to be input.
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.89  2003/06/24 12:30:52  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 1.88  2003/06/23 17:54:56  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    * 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.
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.87  2003/06/18 12:26:01  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    Version 0.96
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
   Also this programme outputs the covariance matrix of the parameters but also    routine fileappend.
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.85  2003/06/17 13:12:43  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    * imach.c (Repository): Check when date of death was earlier that
            Institut national d'études démographiques, Paris.    current date of interview. It may happen when the death was just
   This software have been partly granted by Euro-REVES, a concerted action    prior to the death. In this case, dh was negative and likelihood
   from the European Union.    was wrong (infinity). We still send an "Error" but patch by
   It is copyrighted identically to a GNU software product, ie programme and    assuming that the date of death was just one stepm after the
   software can be distributed freely for non commercial use. Latest version    interview.
   can be accessed at http://euroreves.ined.fr/imach .    (Repository): Because some people have very long ID (first column)
   **********************************************************************/    we changed int to long in num[] and we added a new lvector for
      memory allocation. But we also truncated to 8 characters (left
 #include <math.h>    truncation)
 #include <stdio.h>    (Repository): No more line truncation errors.
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
 #define MAXLINE 256    place. It differs from routine "prevalence" which may be called
 #define GNUPLOTPROGRAM "gnuplot"    many times. Probs is memory consuming and must be used with
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    parcimony.
 #define FILENAMELENGTH 80    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 /*#define DEBUG*/  
 #define windows    Revision 1.83  2003/06/10 13:39:11  lievre
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    *** empty log message ***
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.82  2003/06/05 15:57:20  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Add log in  imach.c and  fullversion number is now printed.
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
   */
 #define NINTERVMAX 8  /*
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */     Interpolated Markov Chain
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Short summary of the programme:
 #define MAXN 20000    
 #define YEARM 12. /* Number of months per year */    This program computes Healthy Life Expectancies from
 #define AGESUP 130    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #define AGEBASE 40    first survey ("cross") where individuals from different ages are
 #ifdef windows    interviewed on their health status or degree of disability (in the
 #define DIRSEPARATOR '\\'    case of a health survey which is our main interest) -2- at least a
 #else    second wave of interviews ("longitudinal") which measure each change
 #define DIRSEPARATOR '/'    (if any) in individual health status.  Health expectancies are
 #endif    computed from the time spent in each health state according to a
     model. More health states you consider, more time is necessary to reach the
 char version[80]="Imach version 0.8h, May 2002, INED-EUROREVES ";    Maximum Likelihood of the parameters involved in the model.  The
 int erreur; /* Error number */    simplest model is the multinomial logistic model where pij is the
 int nvar;    probability to be observed in state j at the second wave
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    conditional to be observed in state i at the first wave. Therefore
 int npar=NPARMAX;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 int nlstate=2; /* Number of live states */    'age' is age and 'sex' is a covariate. If you want to have a more
 int ndeath=1; /* Number of dead states */    complex model than "constant and age", you should modify the program
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    where the markup *Covariates have to be included here again* invites
 int popbased=0;    you to do it.  More covariates you add, slower the
     convergence.
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    The advantage of this computer programme, compared to a simple
 int jmin, jmax; /* min, max spacing between 2 waves */    multinomial logistic model, is clear when the delay between waves is not
 int mle, weightopt;    identical for each individual. Also, if a individual missed an
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    intermediate interview, the information is lost, but taken into
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    account using an interpolation or extrapolation.  
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    hPijx is the probability to be observed in state i at age x+h
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    conditional to the observed state i at age x. The delay 'h' can be
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    split into an exact number (nh*stepm) of unobserved intermediate
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    states. This elementary transition (by month, quarter,
 FILE *fichtm; /* Html File */    semester or year) is modelled as a multinomial logistic.  The hPx
 FILE *ficreseij;    matrix is simply the matrix product of nh*stepm elementary matrices
 char filerese[FILENAMELENGTH];    and the contribution of each individual to the likelihood is simply
 FILE  *ficresvij;    hPijx.
 char fileresv[FILENAMELENGTH];  
 FILE  *ficresvpl;    Also this programme outputs the covariance matrix of the parameters but also
 char fileresvpl[FILENAMELENGTH];    of the life expectancies. It also computes the stable prevalence. 
 char title[MAXLINE];    
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];             Institut national d'études démographiques, Paris.
     This software have been partly granted by Euro-REVES, a concerted action
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
 char filerest[FILENAMELENGTH];    software can be distributed freely for non commercial use. Latest version
 char fileregp[FILENAMELENGTH];    can be accessed at http://euroreves.ined.fr/imach .
 char popfile[FILENAMELENGTH];  
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     
 #define NR_END 1    **********************************************************************/
 #define FREE_ARG char*  /*
 #define FTOL 1.0e-10    main
     read parameterfile
 #define NRANSI    read datafile
 #define ITMAX 200    concatwav
     freqsummary
 #define TOL 2.0e-4    if (mle >= 1)
       mlikeli
 #define CGOLD 0.3819660    print results files
 #define ZEPS 1.0e-10    if mle==1 
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 #define GOLD 1.618034        begin-prev-date,...
 #define GLIMIT 100.0    open gnuplot file
 #define TINY 1.0e-20    open html file
     stable prevalence
 static double maxarg1,maxarg2;     for age prevalim()
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    h Pij x
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    variance of p varprob
      forecasting if prevfcast==1 prevforecast call prevalence()
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    health expectancies
 #define rint(a) floor(a+0.5)    Variance-covariance of DFLE
     prevalence()
 static double sqrarg;     movingaverage()
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    varevsij() 
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    if popbased==1 varevsij(,popbased)
     total life expectancies
 int imx;    Variance of stable prevalence
 int stepm;   end
 /* Stepm, step in month: minimum step interpolation*/  */
   
 int estepm;  
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  
    
 int m,nb;  #include <math.h>
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #include <stdio.h>
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #include <stdlib.h>
 double **pmmij, ***probs, ***mobaverage;  #include <unistd.h>
 double dateintmean=0;  
   #include <sys/time.h>
 double *weight;  #include <time.h>
 int **s; /* Status */  #include "timeval.h"
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define MAXLINE 256
   #define GNUPLOTPROGRAM "gnuplot"
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 double ftolhess; /* Tolerance for computing hessian */  #define FILENAMELENGTH 132
   /*#define DEBUG*/
 /**************** split *************************/  /*#define windows*/
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 {  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define NINTERVMAX 8
    s = strrchr( path,  DIRSEPARATOR );          /* find last / */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
    if ( s == NULL ) {                   /* no directory, so use current */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #if     defined(__bsd__)                /* get current working directory */  #define NCOVMAX 8 /* Maximum number of covariates */
       extern char       *getwd( );  #define MAXN 20000
   #define YEARM 12. /* Number of months per year */
       if ( getwd( dirc ) == NULL ) {  #define AGESUP 130
 #else  #define AGEBASE 40
       extern char       *getcwd( );  #ifdef unix
   #define DIRSEPARATOR '/'
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define ODIRSEPARATOR '\\'
 #endif  #else
          return( GLOCK_ERROR_GETCWD );  #define DIRSEPARATOR '\\'
       }  #define ODIRSEPARATOR '/'
       strcpy( name, path );             /* we've got it */  #endif
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */  /* $Id$ */
       l2 = strlen( s );                 /* length of filename */  /* $State$ */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */  char version[]="Imach version 0.96b, June 2003, INED-EUROREVES ";
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  char fullversion[]="$Revision$ $Date$"; 
       dirc[l1-l2] = 0;                  /* add zero */  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
    }  int nvar;
    l1 = strlen( dirc );                 /* length of directory */  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 #ifdef windows  int npar=NPARMAX;
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  int nlstate=2; /* Number of live states */
 #else  int ndeath=1; /* Number of dead states */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 #endif  int popbased=0;
    s = strrchr( name, '.' );            /* find last / */  
    s++;  int *wav; /* Number of waves for this individuual 0 is possible */
    strcpy(ext,s);                       /* save extension */  int maxwav; /* Maxim number of waves */
    l1= strlen( name);  int jmin, jmax; /* min, max spacing between 2 waves */
    l2= strlen( s)+1;  int gipmx, gsw; /* Global variables on the number of contributions 
    strncpy( finame, name, l1-l2);                     to the likelihood and the sum of weights (done by funcone)*/
    finame[l1-l2]= 0;  int mle, weightopt;
    return( 0 );                         /* we're done */  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 */
   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 */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
 void replace(char *s, char*t)  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 {  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   int i;  FILE *ficlog, *ficrespow;
   int lg=20;  int globpr; /* Global variable for printing or not */
   i=0;  double fretone; /* Only one call to likelihood */
   lg=strlen(t);  long ipmx; /* Number of contributions */
   for(i=0; i<= lg; i++) {  double sw; /* Sum of weights */
     (s[i] = t[i]);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
     if (t[i]== '\\') s[i]='/';  FILE *ficresilk;
   }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 }  FILE *ficresprobmorprev;
   FILE *fichtm, *fichtmcov; /* Html File */
 int nbocc(char *s, char occ)  FILE *ficreseij;
 {  char filerese[FILENAMELENGTH];
   int i,j=0;  FILE  *ficresvij;
   int lg=20;  char fileresv[FILENAMELENGTH];
   i=0;  FILE  *ficresvpl;
   lg=strlen(s);  char fileresvpl[FILENAMELENGTH];
   for(i=0; i<= lg; i++) {  char title[MAXLINE];
   if  (s[i] == occ ) j++;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   }  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   return j;  char tmpout[FILENAMELENGTH]; 
 }  char command[FILENAMELENGTH];
   int  outcmd=0;
 void cutv(char *u,char *v, char*t, char occ)  
 {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   int i,lg,j,p=0;  
   i=0;  char filelog[FILENAMELENGTH]; /* Log file */
   for(j=0; j<=strlen(t)-1; j++) {  char filerest[FILENAMELENGTH];
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  char fileregp[FILENAMELENGTH];
   }  char popfile[FILENAMELENGTH];
   
   lg=strlen(t);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   }  struct timezone tzp;
      u[p]='\0';  extern int gettimeofday();
   struct tm tmg, tm, tmf, *gmtime(), *localtime();
    for(j=0; j<= lg; j++) {  long time_value;
     if (j>=(p+1))(v[j-p-1] = t[j]);  extern long time();
   }  char strcurr[80], strfor[80];
 }  
   #define NR_END 1
 /********************** nrerror ********************/  #define FREE_ARG char*
   #define FTOL 1.0e-10
 void nrerror(char error_text[])  
 {  #define NRANSI 
   fprintf(stderr,"ERREUR ...\n");  #define ITMAX 200 
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  #define TOL 2.0e-4 
 }  
 /*********************** vector *******************/  #define CGOLD 0.3819660 
 double *vector(int nl, int nh)  #define ZEPS 1.0e-10 
 {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #define GOLD 1.618034 
   if (!v) nrerror("allocation failure in vector");  #define GLIMIT 100.0 
   return v-nl+NR_END;  #define TINY 1.0e-20 
 }  
   static double maxarg1,maxarg2;
 /************************ free vector ******************/  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 void free_vector(double*v, int nl, int nh)  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 {    
   free((FREE_ARG)(v+nl-NR_END));  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 }  #define rint(a) floor(a+0.5)
   
 /************************ivector *******************************/  static double sqrarg;
 int *ivector(long nl,long nh)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 {  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  int imx; 
   if (!v) nrerror("allocation failure in ivector");  int stepm;
   return v-nl+NR_END;  /* Stepm, step in month: minimum step interpolation*/
 }  
   int estepm;
 /******************free ivector **************************/  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 void free_ivector(int *v, long nl, long nh)  
 {  int m,nb;
   free((FREE_ARG)(v+nl-NR_END));  long *num;
 }  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 /******************* imatrix *******************************/  double **pmmij, ***probs;
 int **imatrix(long nrl, long nrh, long ncl, long nch)  double dateintmean=0;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {  double *weight;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  int **s; /* Status */
   int **m;  double *agedc, **covar, idx;
    int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   if (!m) nrerror("allocation failure 1 in matrix()");  double ftolhess; /* Tolerance for computing hessian */
   m += NR_END;  
   m -= nrl;  /**************** split *************************/
    static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
    {
   /* allocate rows and set pointers to them */    char  *ss;                            /* pointer */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    int   l1, l2;                         /* length counters */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    l1 = strlen(path );                   /* length of path */
   m[nrl] -= ncl;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
      ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    if ( ss == NULL ) {                   /* no directory, so use current */
        /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   /* return pointer to array of pointers to rows */        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   return m;      /* get current working directory */
 }      /*    extern  char* getcwd ( char *buf , int len);*/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 /****************** free_imatrix *************************/        return( GLOCK_ERROR_GETCWD );
 void free_imatrix(m,nrl,nrh,ncl,nch)      }
       int **m;      strcpy( name, path );               /* we've got it */
       long nch,ncl,nrh,nrl;    } else {                              /* strip direcotry from path */
      /* free an int matrix allocated by imatrix() */      ss++;                               /* after this, the filename */
 {      l2 = strlen( ss );                  /* length of filename */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   free((FREE_ARG) (m+nrl-NR_END));      strcpy( name, ss );         /* save file name */
 }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
 /******************* matrix *******************************/    }
 double **matrix(long nrl, long nrh, long ncl, long nch)    l1 = strlen( dirc );                  /* length of directory */
 {    /*#ifdef windows
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   double **m;  #else
     if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #endif
   if (!m) nrerror("allocation failure 1 in matrix()");    */
   m += NR_END;    ss = strrchr( name, '.' );            /* find last / */
   m -= nrl;    ss++;
     strcpy(ext,ss);                       /* save extension */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    l1= strlen( name);
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    l2= strlen(ss)+1;
   m[nrl] += NR_END;    strncpy( finame, name, l1-l2);
   m[nrl] -= ncl;    finame[l1-l2]= 0;
     return( 0 );                          /* we're done */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  }
   return m;  
 }  
   /******************************************/
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  void replace_back_to_slash(char *s, char*t)
 {  {
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    int i;
   free((FREE_ARG)(m+nrl-NR_END));    int lg=0;
 }    i=0;
     lg=strlen(t);
 /******************* ma3x *******************************/    for(i=0; i<= lg; i++) {
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)      (s[i] = t[i]);
 {      if (t[i]== '\\') s[i]='/';
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    }
   double ***m;  }
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int nbocc(char *s, char occ)
   if (!m) nrerror("allocation failure 1 in matrix()");  {
   m += NR_END;    int i,j=0;
   m -= nrl;    int lg=20;
     i=0;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    lg=strlen(s);
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    for(i=0; i<= lg; i++) {
   m[nrl] += NR_END;    if  (s[i] == occ ) j++;
   m[nrl] -= ncl;    }
     return j;
   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)));  void cutv(char *u,char *v, char*t, char occ)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  {
   m[nrl][ncl] += NR_END;    /* cuts string t into u and v where u is ended by char occ excluding it
   m[nrl][ncl] -= nll;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   for (j=ncl+1; j<=nch; j++)       gives u="abcedf" and v="ghi2j" */
     m[nrl][j]=m[nrl][j-1]+nlay;    int i,lg,j,p=0;
      i=0;
   for (i=nrl+1; i<=nrh; i++) {    for(j=0; j<=strlen(t)-1; j++) {
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     for (j=ncl+1; j<=nch; j++)    }
       m[i][j]=m[i][j-1]+nlay;  
   }    lg=strlen(t);
   return m;    for(j=0; j<p; j++) {
 }      (u[j] = t[j]);
     }
 /*************************free ma3x ************************/       u[p]='\0';
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {     for(j=0; j<= lg; j++) {
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));      if (j>=(p+1))(v[j-p-1] = t[j]);
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    }
   free((FREE_ARG)(m+nrl-NR_END));  }
 }  
   /********************** nrerror ********************/
 /***************** f1dim *************************/  
 extern int ncom;  void nrerror(char error_text[])
 extern double *pcom,*xicom;  {
 extern double (*nrfunc)(double []);    fprintf(stderr,"ERREUR ...\n");
      fprintf(stderr,"%s\n",error_text);
 double f1dim(double x)    exit(EXIT_FAILURE);
 {  }
   int j;  /*********************** vector *******************/
   double f;  double *vector(int nl, int nh)
   double *xt;  {
      double *v;
   xt=vector(1,ncom);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    if (!v) nrerror("allocation failure in vector");
   f=(*nrfunc)(xt);    return v-nl+NR_END;
   free_vector(xt,1,ncom);  }
   return f;  
 }  /************************ free vector ******************/
   void free_vector(double*v, int nl, int nh)
 /*****************brent *************************/  {
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    free((FREE_ARG)(v+nl-NR_END));
 {  }
   int iter;  
   double a,b,d,etemp;  /************************ivector *******************************/
   double fu,fv,fw,fx;  int *ivector(long nl,long nh)
   double ftemp;  {
   double p,q,r,tol1,tol2,u,v,w,x,xm;    int *v;
   double e=0.0;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
      if (!v) nrerror("allocation failure in ivector");
   a=(ax < cx ? ax : cx);    return v-nl+NR_END;
   b=(ax > cx ? ax : cx);  }
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);  /******************free ivector **************************/
   for (iter=1;iter<=ITMAX;iter++) {  void free_ivector(int *v, long nl, long nh)
     xm=0.5*(a+b);  {
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    free((FREE_ARG)(v+nl-NR_END));
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  }
     printf(".");fflush(stdout);  
 #ifdef DEBUG  /************************lvector *******************************/
     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);  long *lvector(long nl,long nh)
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  {
 #endif    long *v;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       *xmin=x;    if (!v) nrerror("allocation failure in ivector");
       return fx;    return v-nl+NR_END;
     }  }
     ftemp=fu;  
     if (fabs(e) > tol1) {  /******************free lvector **************************/
       r=(x-w)*(fx-fv);  void free_lvector(long *v, long nl, long nh)
       q=(x-v)*(fx-fw);  {
       p=(x-v)*q-(x-w)*r;    free((FREE_ARG)(v+nl-NR_END));
       q=2.0*(q-r);  }
       if (q > 0.0) p = -p;  
       q=fabs(q);  /******************* imatrix *******************************/
       etemp=e;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       e=d;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       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));    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       else {    int **m; 
         d=p/q;    
         u=x+d;    /* allocate pointers to rows */ 
         if (u-a < tol2 || b-u < tol2)    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
           d=SIGN(tol1,xm-x);    if (!m) nrerror("allocation failure 1 in matrix()"); 
       }    m += NR_END; 
     } else {    m -= nrl; 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    
     }    
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    /* allocate rows and set pointers to them */ 
     fu=(*f)(u);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     if (fu <= fx) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       if (u >= x) a=x; else b=x;    m[nrl] += NR_END; 
       SHFT(v,w,x,u)    m[nrl] -= ncl; 
         SHFT(fv,fw,fx,fu)    
         } else {    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
           if (u < x) a=u; else b=u;    
           if (fu <= fw || w == x) {    /* return pointer to array of pointers to rows */ 
             v=w;    return m; 
             w=u;  } 
             fv=fw;  
             fw=fu;  /****************** free_imatrix *************************/
           } else if (fu <= fv || v == x || v == w) {  void free_imatrix(m,nrl,nrh,ncl,nch)
             v=u;        int **m;
             fv=fu;        long nch,ncl,nrh,nrl; 
           }       /* free an int matrix allocated by imatrix() */ 
         }  { 
   }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   nrerror("Too many iterations in brent");    free((FREE_ARG) (m+nrl-NR_END)); 
   *xmin=x;  } 
   return fx;  
 }  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
 /****************** mnbrak ***********************/  {
     long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    double **m;
             double (*func)(double))  
 {    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double ulim,u,r,q, dum;    if (!m) nrerror("allocation failure 1 in matrix()");
   double fu;    m += NR_END;
      m -= nrl;
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   if (*fb > *fa) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     SHFT(dum,*ax,*bx,dum)    m[nrl] += NR_END;
       SHFT(dum,*fb,*fa,dum)    m[nrl] -= ncl;
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   *fc=(*func)(*cx);    return m;
   while (*fb > *fc) {    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     r=(*bx-*ax)*(*fb-*fc);     */
     q=(*bx-*cx)*(*fb-*fa);  }
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  /*************************free matrix ************************/
     ulim=(*bx)+GLIMIT*(*cx-*bx);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     if ((*bx-u)*(u-*cx) > 0.0) {  {
       fu=(*func)(u);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     } else if ((*cx-u)*(u-ulim) > 0.0) {    free((FREE_ARG)(m+nrl-NR_END));
       fu=(*func)(u);  }
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  /******************* ma3x *******************************/
           SHFT(*fb,*fc,fu,(*func)(u))  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
           }  {
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       u=ulim;    double ***m;
       fu=(*func)(u);  
     } else {    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       u=(*cx)+GOLD*(*cx-*bx);    if (!m) nrerror("allocation failure 1 in matrix()");
       fu=(*func)(u);    m += NR_END;
     }    m -= nrl;
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 }    m[nrl] += NR_END;
     m[nrl] -= ncl;
 /*************** linmin ************************/  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 int ncom;  
 double *pcom,*xicom;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 double (*nrfunc)(double []);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
      m[nrl][ncl] += NR_END;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    m[nrl][ncl] -= nll;
 {    for (j=ncl+1; j<=nch; j++) 
   double brent(double ax, double bx, double cx,      m[nrl][j]=m[nrl][j-1]+nlay;
                double (*f)(double), double tol, double *xmin);    
   double f1dim(double x);    for (i=nrl+1; i<=nrh; i++) {
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
               double *fc, double (*func)(double));      for (j=ncl+1; j<=nch; j++) 
   int j;        m[i][j]=m[i][j-1]+nlay;
   double xx,xmin,bx,ax;    }
   double fx,fb,fa;    return m; 
      /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   ncom=n;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   pcom=vector(1,n);    */
   xicom=vector(1,n);  }
   nrfunc=func;  
   for (j=1;j<=n;j++) {  /*************************free ma3x ************************/
     pcom[j]=p[j];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     xicom[j]=xi[j];  {
   }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   ax=0.0;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   xx=1.0;    free((FREE_ARG)(m+nrl-NR_END));
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  }
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  /*************** function subdirf ***********/
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  char *subdirf(char fileres[])
 #endif  {
   for (j=1;j<=n;j++) {    /* Caution optionfilefiname is hidden */
     xi[j] *= xmin;    strcpy(tmpout,optionfilefiname);
     p[j] += xi[j];    strcat(tmpout,"/"); /* Add to the right */
   }    strcat(tmpout,fileres);
   free_vector(xicom,1,n);    return tmpout;
   free_vector(pcom,1,n);  }
 }  
   /*************** function subdirf2 ***********/
 /*************** powell ************************/  char *subdirf2(char fileres[], char *preop)
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  {
             double (*func)(double []))    
 {    /* Caution optionfilefiname is hidden */
   void linmin(double p[], double xi[], int n, double *fret,    strcpy(tmpout,optionfilefiname);
               double (*func)(double []));    strcat(tmpout,"/");
   int i,ibig,j;    strcat(tmpout,preop);
   double del,t,*pt,*ptt,*xit;    strcat(tmpout,fileres);
   double fp,fptt;    return tmpout;
   double *xits;  }
   pt=vector(1,n);  
   ptt=vector(1,n);  /*************** function subdirf3 ***********/
   xit=vector(1,n);  char *subdirf3(char fileres[], char *preop, char *preop2)
   xits=vector(1,n);  {
   *fret=(*func)(p);    
   for (j=1;j<=n;j++) pt[j]=p[j];    /* Caution optionfilefiname is hidden */
   for (*iter=1;;++(*iter)) {    strcpy(tmpout,optionfilefiname);
     fp=(*fret);    strcat(tmpout,"/");
     ibig=0;    strcat(tmpout,preop);
     del=0.0;    strcat(tmpout,preop2);
     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++) {  /***************** f1dim *************************/
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  extern int ncom; 
       fptt=(*fret);  extern double *pcom,*xicom;
 #ifdef DEBUG  extern double (*nrfunc)(double []); 
       printf("fret=%lf \n",*fret);   
 #endif  double f1dim(double x) 
       printf("%d",i);fflush(stdout);  { 
       linmin(p,xit,n,fret,func);    int j; 
       if (fabs(fptt-(*fret)) > del) {    double f;
         del=fabs(fptt-(*fret));    double *xt; 
         ibig=i;   
       }    xt=vector(1,ncom); 
 #ifdef DEBUG    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       printf("%d %.12e",i,(*fret));    f=(*nrfunc)(xt); 
       for (j=1;j<=n;j++) {    free_vector(xt,1,ncom); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    return f; 
         printf(" x(%d)=%.12e",j,xit[j]);  } 
       }  
       for(j=1;j<=n;j++)  /*****************brent *************************/
         printf(" p=%.12e",p[j]);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       printf("\n");  { 
 #endif    int iter; 
     }    double a,b,d,etemp;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    double fu,fv,fw,fx;
 #ifdef DEBUG    double ftemp;
       int k[2],l;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       k[0]=1;    double e=0.0; 
       k[1]=-1;   
       printf("Max: %.12e",(*func)(p));    a=(ax < cx ? ax : cx); 
       for (j=1;j<=n;j++)    b=(ax > cx ? ax : cx); 
         printf(" %.12e",p[j]);    x=w=v=bx; 
       printf("\n");    fw=fv=fx=(*f)(x); 
       for(l=0;l<=1;l++) {    for (iter=1;iter<=ITMAX;iter++) { 
         for (j=1;j<=n;j++) {      xm=0.5*(a+b); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         }      printf(".");fflush(stdout);
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));      fprintf(ficlog,".");fflush(ficlog);
       }  #ifdef DEBUG
 #endif      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       free_vector(xit,1,n);  #endif
       free_vector(xits,1,n);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       free_vector(ptt,1,n);        *xmin=x; 
       free_vector(pt,1,n);        return fx; 
       return;      } 
     }      ftemp=fu;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");      if (fabs(e) > tol1) { 
     for (j=1;j<=n;j++) {        r=(x-w)*(fx-fv); 
       ptt[j]=2.0*p[j]-pt[j];        q=(x-v)*(fx-fw); 
       xit[j]=p[j]-pt[j];        p=(x-v)*q-(x-w)*r; 
       pt[j]=p[j];        q=2.0*(q-r); 
     }        if (q > 0.0) p = -p; 
     fptt=(*func)(ptt);        q=fabs(q); 
     if (fptt < fp) {        etemp=e; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        e=d; 
       if (t < 0.0) {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         linmin(p,xit,n,fret,func);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         for (j=1;j<=n;j++) {        else { 
           xi[j][ibig]=xi[j][n];          d=p/q; 
           xi[j][n]=xit[j];          u=x+d; 
         }          if (u-a < tol2 || b-u < tol2) 
 #ifdef DEBUG            d=SIGN(tol1,xm-x); 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        } 
         for(j=1;j<=n;j++)      } else { 
           printf(" %.12e",xit[j]);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         printf("\n");      } 
 #endif      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       }      fu=(*f)(u); 
     }      if (fu <= fx) { 
   }        if (u >= x) a=x; else b=x; 
 }        SHFT(v,w,x,u) 
           SHFT(fv,fw,fx,fu) 
 /**** Prevalence limit ****************/          } else { 
             if (u < x) a=u; else b=u; 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)            if (fu <= fw || w == x) { 
 {              v=w; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit              w=u; 
      matrix by transitions matrix until convergence is reached */              fv=fw; 
               fw=fu; 
   int i, ii,j,k;            } else if (fu <= fv || v == x || v == w) { 
   double min, max, maxmin, maxmax,sumnew=0.;              v=u; 
   double **matprod2();              fv=fu; 
   double **out, cov[NCOVMAX], **pmij();            } 
   double **newm;          } 
   double agefin, delaymax=50 ; /* Max number of years to converge */    } 
     nrerror("Too many iterations in brent"); 
   for (ii=1;ii<=nlstate+ndeath;ii++)    *xmin=x; 
     for (j=1;j<=nlstate+ndeath;j++){    return fx; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  } 
     }  
   /****************** mnbrak ***********************/
    cov[1]=1.;  
    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */              double (*func)(double)) 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  { 
     newm=savm;    double ulim,u,r,q, dum;
     /* Covariates have to be included here again */    double fu; 
      cov[2]=agefin;   
      *fa=(*func)(*ax); 
       for (k=1; k<=cptcovn;k++) {    *fb=(*func)(*bx); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    if (*fb > *fa) { 
         /*      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]]);*/      SHFT(dum,*ax,*bx,dum) 
       }        SHFT(dum,*fb,*fa,dum) 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        } 
       for (k=1; k<=cptcovprod;k++)    *cx=(*bx)+GOLD*(*bx-*ax); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    *fc=(*func)(*cx); 
     while (*fb > *fc) { 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      r=(*bx-*ax)*(*fb-*fc); 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      q=(*bx-*cx)*(*fb-*fa); 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
     savm=oldm;      if ((*bx-u)*(u-*cx) > 0.0) { 
     oldm=newm;        fu=(*func)(u); 
     maxmax=0.;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     for(j=1;j<=nlstate;j++){        fu=(*func)(u); 
       min=1.;        if (fu < *fc) { 
       max=0.;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       for(i=1; i<=nlstate; i++) {            SHFT(*fb,*fc,fu,(*func)(u)) 
         sumnew=0;            } 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         prlim[i][j]= newm[i][j]/(1-sumnew);        u=ulim; 
         max=FMAX(max,prlim[i][j]);        fu=(*func)(u); 
         min=FMIN(min,prlim[i][j]);      } else { 
       }        u=(*cx)+GOLD*(*cx-*bx); 
       maxmin=max-min;        fu=(*func)(u); 
       maxmax=FMAX(maxmax,maxmin);      } 
     }      SHFT(*ax,*bx,*cx,u) 
     if(maxmax < ftolpl){        SHFT(*fa,*fb,*fc,fu) 
       return prlim;        } 
     }  } 
   }  
 }  /*************** linmin ************************/
   
 /*************** transition probabilities ***************/  int ncom; 
   double *pcom,*xicom;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  double (*nrfunc)(double []); 
 {   
   double s1, s2;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   /*double t34;*/  { 
   int i,j,j1, nc, ii, jj;    double brent(double ax, double bx, double cx, 
                  double (*f)(double), double tol, double *xmin); 
     for(i=1; i<= nlstate; i++){    double f1dim(double x); 
     for(j=1; j<i;j++){    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){                double *fc, double (*func)(double)); 
         /*s2 += param[i][j][nc]*cov[nc];*/    int j; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    double xx,xmin,bx,ax; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    double fx,fb,fa;
       }   
       ps[i][j]=s2;    ncom=n; 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    pcom=vector(1,n); 
     }    xicom=vector(1,n); 
     for(j=i+1; j<=nlstate+ndeath;j++){    nrfunc=func; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    for (j=1;j<=n;j++) { 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      pcom[j]=p[j]; 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      xicom[j]=xi[j]; 
       }    } 
       ps[i][j]=s2;    ax=0.0; 
     }    xx=1.0; 
   }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     /*ps[3][2]=1;*/    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   #ifdef DEBUG
   for(i=1; i<= nlstate; i++){    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
      s1=0;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     for(j=1; j<i; j++)  #endif
       s1+=exp(ps[i][j]);    for (j=1;j<=n;j++) { 
     for(j=i+1; j<=nlstate+ndeath; j++)      xi[j] *= xmin; 
       s1+=exp(ps[i][j]);      p[j] += xi[j]; 
     ps[i][i]=1./(s1+1.);    } 
     for(j=1; j<i; j++)    free_vector(xicom,1,n); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    free_vector(pcom,1,n); 
     for(j=i+1; j<=nlstate+ndeath; j++)  } 
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  char *asc_diff_time(long time_sec, char ascdiff[])
   } /* end i */  {
     long sec_left, days, hours, minutes;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    days = (time_sec) / (60*60*24);
     for(jj=1; jj<= nlstate+ndeath; jj++){    sec_left = (time_sec) % (60*60*24);
       ps[ii][jj]=0;    hours = (sec_left) / (60*60) ;
       ps[ii][ii]=1;    sec_left = (sec_left) %(60*60);
     }    minutes = (sec_left) /60;
   }    sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     return ascdiff;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  }
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  /*************** powell ************************/
    }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     printf("\n ");              double (*func)(double [])) 
     }  { 
     printf("\n ");printf("%lf ",cov[2]);*/    void linmin(double p[], double xi[], int n, double *fret, 
 /*                double (*func)(double [])); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    int i,ibig,j; 
   goto end;*/    double del,t,*pt,*ptt,*xit;
     return ps;    double fp,fptt;
 }    double *xits;
     int niterf, itmp;
 /**************** Product of 2 matrices ******************/  
     pt=vector(1,n); 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    ptt=vector(1,n); 
 {    xit=vector(1,n); 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    xits=vector(1,n); 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    *fret=(*func)(p); 
   /* in, b, out are matrice of pointers which should have been initialized    for (j=1;j<=n;j++) pt[j]=p[j]; 
      before: only the contents of out is modified. The function returns    for (*iter=1;;++(*iter)) { 
      a pointer to pointers identical to out */      fp=(*fret); 
   long i, j, k;      ibig=0; 
   for(i=nrl; i<= nrh; i++)      del=0.0; 
     for(k=ncolol; k<=ncoloh; k++)      last_time=curr_time;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      (void) gettimeofday(&curr_time,&tzp);
         out[i][k] +=in[i][j]*b[j][k];      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
       fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
   return out;      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
 }      for (i=1;i<=n;i++) {
         printf(" %d %.12f",i, p[i]);
         fprintf(ficlog," %d %.12lf",i, p[i]);
 /************* Higher Matrix Product ***************/        fprintf(ficrespow," %.12lf", p[i]);
       }
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      printf("\n");
 {      fprintf(ficlog,"\n");
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      fprintf(ficrespow,"\n");fflush(ficrespow);
      duration (i.e. until      if(*iter <=3){
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        tm = *localtime(&curr_time.tv_sec);
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        strcpy(strcurr,asctime(&tmf));
      (typically every 2 years instead of every month which is too big).  /*       asctime_r(&tm,strcurr); */
      Model is determined by parameters x and covariates have to be        forecast_time=curr_time;
      included manually here.        itmp = strlen(strcurr);
         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);
   int i, j, d, h, k;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   double **out, cov[NCOVMAX];        for(niterf=10;niterf<=30;niterf+=10){
   double **newm;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
           tmf = *localtime(&forecast_time.tv_sec);
   /* Hstepm could be zero and should return the unit matrix */  /*      asctime_r(&tmf,strfor); */
   for (i=1;i<=nlstate+ndeath;i++)          strcpy(strfor,asctime(&tmf));
     for (j=1;j<=nlstate+ndeath;j++){          itmp = strlen(strfor);
       oldm[i][j]=(i==j ? 1.0 : 0.0);          if(strfor[itmp-1]=='\n')
       po[i][j][0]=(i==j ? 1.0 : 0.0);          strfor[itmp-1]='\0';
     }          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);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */          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);
   for(h=1; h <=nhstepm; h++){        }
     for(d=1; d <=hstepm; d++){      }
       newm=savm;      for (i=1;i<=n;i++) { 
       /* Covariates have to be included here again */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       cov[1]=1.;        fptt=(*fret); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  #ifdef DEBUG
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        printf("fret=%lf \n",*fret);
       for (k=1; k<=cptcovage;k++)        fprintf(ficlog,"fret=%lf \n",*fret);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  #endif
       for (k=1; k<=cptcovprod;k++)        printf("%d",i);fflush(stdout);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        fprintf(ficlog,"%d",i);fflush(ficlog);
         linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/          del=fabs(fptt-(*fret)); 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/          ibig=i; 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        } 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  #ifdef DEBUG
       savm=oldm;        printf("%d %.12e",i,(*fret));
       oldm=newm;        fprintf(ficlog,"%d %.12e",i,(*fret));
     }        for (j=1;j<=n;j++) {
     for(i=1; i<=nlstate+ndeath; i++)          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       for(j=1;j<=nlstate+ndeath;j++) {          printf(" x(%d)=%.12e",j,xit[j]);
         po[i][j][h]=newm[i][j];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        }
          */        for(j=1;j<=n;j++) {
       }          printf(" p=%.12e",p[j]);
   } /* end h */          fprintf(ficlog," p=%.12e",p[j]);
   return po;        }
 }        printf("\n");
         fprintf(ficlog,"\n");
   #endif
 /*************** log-likelihood *************/      } 
 double func( double *x)      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
 {  #ifdef DEBUG
   int i, ii, j, k, mi, d, kk;        int k[2],l;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        k[0]=1;
   double **out;        k[1]=-1;
   double sw; /* Sum of weights */        printf("Max: %.12e",(*func)(p));
   double lli; /* Individual log likelihood */        fprintf(ficlog,"Max: %.12e",(*func)(p));
   long ipmx;        for (j=1;j<=n;j++) {
   /*extern weight */          printf(" %.12e",p[j]);
   /* We are differentiating ll according to initial status */          fprintf(ficlog," %.12e",p[j]);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        }
   /*for(i=1;i<imx;i++)        printf("\n");
     printf(" %d\n",s[4][i]);        fprintf(ficlog,"\n");
   */        for(l=0;l<=1;l++) {
   cov[1]=1.;          for (j=1;j<=n;j++) {
             ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   for(k=1; k<=nlstate; k++) ll[k]=0.;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];          }
     for(mi=1; mi<= wav[i]-1; mi++){          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       for (ii=1;ii<=nlstate+ndeath;ii++)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        }
       for(d=0; d<dh[mi][i]; d++){  #endif
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
         for (kk=1; kk<=cptcovage;kk++) {        free_vector(xit,1,n); 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        free_vector(xits,1,n); 
         }        free_vector(ptt,1,n); 
                free_vector(pt,1,n); 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        return; 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      } 
         savm=oldm;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
         oldm=newm;      for (j=1;j<=n;j++) { 
                ptt[j]=2.0*p[j]-pt[j]; 
                xit[j]=p[j]-pt[j]; 
       } /* end mult */        pt[j]=p[j]; 
            } 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      fptt=(*func)(ptt); 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      if (fptt < fp) { 
       ipmx +=1;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       sw += weight[i];        if (t < 0.0) { 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          linmin(p,xit,n,fret,func); 
     } /* end of wave */          for (j=1;j<=n;j++) { 
   } /* end of individual */            xi[j][ibig]=xi[j][n]; 
             xi[j][n]=xit[j]; 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];          }
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  #ifdef DEBUG
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   return -l;          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++){
             printf(" %.12e",xit[j]);
             fprintf(ficlog," %.12e",xit[j]);
 /*********** Maximum Likelihood Estimation ***************/          }
           printf("\n");
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))          fprintf(ficlog,"\n");
 {  #endif
   int i,j, iter;        }
   double **xi,*delti;      } 
   double fret;    } 
   xi=matrix(1,npar,1,npar);  } 
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)  /**** Prevalence limit (stable prevalence)  ****************/
       xi[i][j]=(i==j ? 1.0 : 0.0);  
   printf("Powell\n");  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   powell(p,xi,npar,ftol,&iter,&fret,func);  {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));       matrix by transitions matrix until convergence is reached */
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  
     int i, ii,j,k;
 }    double min, max, maxmin, maxmax,sumnew=0.;
     double **matprod2();
 /**** Computes Hessian and covariance matrix ***/    double **out, cov[NCOVMAX], **pmij();
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    double **newm;
 {    double agefin, delaymax=50 ; /* Max number of years to converge */
   double  **a,**y,*x,pd;  
   double **hess;    for (ii=1;ii<=nlstate+ndeath;ii++)
   int i, j,jk;      for (j=1;j<=nlstate+ndeath;j++){
   int *indx;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);     cov[1]=1.;
   void lubksb(double **a, int npar, int *indx, double b[]) ;   
   void ludcmp(double **a, int npar, int *indx, double *d) ;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   hess=matrix(1,npar,1,npar);      newm=savm;
       /* Covariates have to be included here again */
   printf("\nCalculation of the hessian matrix. Wait...\n");       cov[2]=agefin;
   for (i=1;i<=npar;i++){    
     printf("%d",i);fflush(stdout);        for (k=1; k<=cptcovn;k++) {
     hess[i][i]=hessii(p,ftolhess,i,delti);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     /*printf(" %f ",p[i]);*/          /*      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]]);*/
     /*printf(" %lf ",hess[i][i]);*/        }
   }        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
          for (k=1; k<=cptcovprod;k++)
   for (i=1;i<=npar;i++) {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     for (j=1;j<=npar;j++)  {  
       if (j>i) {        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         printf(".%d%d",i,j);fflush(stdout);        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         hess[i][j]=hessij(p,delti,i,j);        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
         hess[j][i]=hess[i][j];          out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
         /*printf(" %lf ",hess[i][j]);*/  
       }      savm=oldm;
     }      oldm=newm;
   }      maxmax=0.;
   printf("\n");      for(j=1;j<=nlstate;j++){
         min=1.;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        max=0.;
          for(i=1; i<=nlstate; i++) {
   a=matrix(1,npar,1,npar);          sumnew=0;
   y=matrix(1,npar,1,npar);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   x=vector(1,npar);          prlim[i][j]= newm[i][j]/(1-sumnew);
   indx=ivector(1,npar);          max=FMAX(max,prlim[i][j]);
   for (i=1;i<=npar;i++)          min=FMIN(min,prlim[i][j]);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        }
   ludcmp(a,npar,indx,&pd);        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++){    }
       matcov[i][j]=x[i];  }
     }  
   }  /*************** transition probabilities ***************/ 
   
   printf("\n#Hessian matrix#\n");  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   for (i=1;i<=npar;i++) {  {
     for (j=1;j<=npar;j++) {    double s1, s2;
       printf("%.3e ",hess[i][j]);    /*double t34;*/
     }    int i,j,j1, nc, ii, jj;
     printf("\n");  
   }      for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){
   /* Recompute Inverse */        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   for (i=1;i<=npar;i++)          /*s2 += param[i][j][nc]*cov[nc];*/
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   ludcmp(a,npar,indx,&pd);          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         }
   /*  printf("\n#Hessian matrix recomputed#\n");        ps[i][j]=s2;
         /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   for (j=1;j<=npar;j++) {      }
     for (i=1;i<=npar;i++) x[i]=0;      for(j=i+1; j<=nlstate+ndeath;j++){
     x[j]=1;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     lubksb(a,npar,indx,x);          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     for (i=1;i<=npar;i++){          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
       y[i][j]=x[i];        }
       printf("%.3e ",y[i][j]);        ps[i][j]=s2;
     }      }
     printf("\n");    }
   }      /*ps[3][2]=1;*/
   */  
     for(i=1; i<= nlstate; i++){
   free_matrix(a,1,npar,1,npar);       s1=0;
   free_matrix(y,1,npar,1,npar);      for(j=1; j<i; j++)
   free_vector(x,1,npar);        s1+=exp(ps[i][j]);
   free_ivector(indx,1,npar);      for(j=i+1; j<=nlstate+ndeath; j++)
   free_matrix(hess,1,npar,1,npar);        s1+=exp(ps[i][j]);
       ps[i][i]=1./(s1+1.);
       for(j=1; j<i; j++)
 }        ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=i+1; j<=nlstate+ndeath; j++)
 /*************** hessian matrix ****************/        ps[i][j]= exp(ps[i][j])*ps[i][i];
 double hessii( double x[], double delta, int theta, double delti[])      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
 {    } /* end i */
   int i;  
   int l=1, lmax=20;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   double k1,k2;      for(jj=1; jj<= nlstate+ndeath; jj++){
   double p2[NPARMAX+1];        ps[ii][jj]=0;
   double res;        ps[ii][ii]=1;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      }
   double fx;    }
   int k=0,kmax=10;  
   double l1;  
     /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   fx=func(x);      for(jj=1; jj<= nlstate+ndeath; jj++){
   for (i=1;i<=npar;i++) p2[i]=x[i];       printf("%lf ",ps[ii][jj]);
   for(l=0 ; l <=lmax; l++){     }
     l1=pow(10,l);      printf("\n ");
     delts=delt;      }
     for(k=1 ; k <kmax; k=k+1){      printf("\n ");printf("%lf ",cov[2]);*/
       delt = delta*(l1*k);  /*
       p2[theta]=x[theta] +delt;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
       k1=func(p2)-fx;    goto end;*/
       p2[theta]=x[theta]-delt;      return ps;
       k2=func(p2)-fx;  }
       /*res= (k1-2.0*fx+k2)/delt/delt; */  
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  /**************** Product of 2 matrices ******************/
        
 #ifdef DEBUG  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  {
 #endif    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    /* in, b, out are matrice of pointers which should have been initialized 
         k=kmax;       before: only the contents of out is modified. The function returns
       }       a pointer to pointers identical to out */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    long i, j, k;
         k=kmax; l=lmax*10.;    for(i=nrl; i<= nrh; i++)
       }      for(k=ncolol; k<=ncoloh; k++)
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        for(j=ncl,out[i][k]=0.; j<=nch; j++)
         delts=delt;          out[i][k] +=in[i][j]*b[j][k];
       }  
     }    return out;
   }  }
   delti[theta]=delts;  
   return res;  
    /************* Higher Matrix Product ***************/
 }  
   double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
 double hessij( double x[], double delti[], int thetai,int thetaj)  {
 {    /* Computes the transition matrix starting at age 'age' over 
   int i;       'nhstepm*hstepm*stepm' months (i.e. until
   int l=1, l1, lmax=20;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   double k1,k2,k3,k4,res,fx;       nhstepm*hstepm matrices. 
   double p2[NPARMAX+1];       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   int k;       (typically every 2 years instead of every month which is too big 
        for the memory).
   fx=func(x);       Model is determined by parameters x and covariates have to be 
   for (k=1; k<=2; k++) {       included manually here. 
     for (i=1;i<=npar;i++) p2[i]=x[i];  
     p2[thetai]=x[thetai]+delti[thetai]/k;       */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k1=func(p2)-fx;    int i, j, d, h, k;
      double **out, cov[NCOVMAX];
     p2[thetai]=x[thetai]+delti[thetai]/k;    double **newm;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k2=func(p2)-fx;    /* Hstepm could be zero and should return the unit matrix */
      for (i=1;i<=nlstate+ndeath;i++)
     p2[thetai]=x[thetai]-delti[thetai]/k;      for (j=1;j<=nlstate+ndeath;j++){
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        oldm[i][j]=(i==j ? 1.0 : 0.0);
     k3=func(p2)-fx;        po[i][j][0]=(i==j ? 1.0 : 0.0);
        }
     p2[thetai]=x[thetai]-delti[thetai]/k;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    for(h=1; h <=nhstepm; h++){
     k4=func(p2)-fx;      for(d=1; d <=hstepm; d++){
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        newm=savm;
 #ifdef DEBUG        /* Covariates have to be included here again */
     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);        cov[1]=1.;
 #endif        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   }        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   return res;        for (k=1; k<=cptcovage;k++)
 }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
 /************** Inverse of matrix **************/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 void ludcmp(double **a, int n, int *indx, double *d)  
 {  
   int i,imax,j,k;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   double big,dum,sum,temp;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   double *vv;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                       pmij(pmmij,cov,ncovmodel,x,nlstate));
   vv=vector(1,n);        savm=oldm;
   *d=1.0;        oldm=newm;
   for (i=1;i<=n;i++) {      }
     big=0.0;      for(i=1; i<=nlstate+ndeath; i++)
     for (j=1;j<=n;j++)        for(j=1;j<=nlstate+ndeath;j++) {
       if ((temp=fabs(a[i][j])) > big) big=temp;          po[i][j][h]=newm[i][j];
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     vv[i]=1.0/big;           */
   }        }
   for (j=1;j<=n;j++) {    } /* end h */
     for (i=1;i<j;i++) {    return po;
       sum=a[i][j];  }
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;  
     }  /*************** log-likelihood *************/
     big=0.0;  double func( double *x)
     for (i=j;i<=n;i++) {  {
       sum=a[i][j];    int i, ii, j, k, mi, d, kk;
       for (k=1;k<j;k++)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         sum -= a[i][k]*a[k][j];    double **out;
       a[i][j]=sum;    double sw; /* Sum of weights */
       if ( (dum=vv[i]*fabs(sum)) >= big) {    double lli; /* Individual log likelihood */
         big=dum;    int s1, s2;
         imax=i;    double bbh, survp;
       }    long ipmx;
     }    /*extern weight */
     if (j != imax) {    /* We are differentiating ll according to initial status */
       for (k=1;k<=n;k++) {    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         dum=a[imax][k];    /*for(i=1;i<imx;i++) 
         a[imax][k]=a[j][k];      printf(" %d\n",s[4][i]);
         a[j][k]=dum;    */
       }    cov[1]=1.;
       *d = -(*d);  
       vv[imax]=vv[j];    for(k=1; k<=nlstate; k++) ll[k]=0.;
     }  
     indx[j]=imax;    if(mle==1){
     if (a[j][j] == 0.0) a[j][j]=TINY;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     if (j != n) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       dum=1.0/(a[j][j]);        for(mi=1; mi<= wav[i]-1; mi++){
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          for (ii=1;ii<=nlstate+ndeath;ii++)
     }            for (j=1;j<=nlstate+ndeath;j++){
   }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(vv,1,n);  /* Doesn't work */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 ;            }
 }          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
 void lubksb(double **a, int n, int *indx, double b[])            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 {            for (kk=1; kk<=cptcovage;kk++) {
   int i,ii=0,ip,j;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double sum;            }
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for (i=1;i<=n;i++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     ip=indx[i];            savm=oldm;
     sum=b[ip];            oldm=newm;
     b[ip]=b[i];          } /* end mult */
     if (ii)        
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     else if (sum) ii=i;          /* But now since version 0.9 we anticipate for bias and large stepm.
     b[i]=sum;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   }           * (in months) between two waves is not a multiple of stepm, we rounded to 
   for (i=n;i>=1;i--) {           * the nearest (and in case of equal distance, to the lowest) interval but now
     sum=b[i];           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     b[i]=sum/a[i][i];           * 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
 }           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
 /************ Frequencies ********************/           * For stepm > 1 the results are less biased than in previous versions. 
 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,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)           */
 {  /* Some frequencies */          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          bbh=(double)bh[mi][i]/(double)stepm; 
   double ***freq; /* Frequencies */          /* bias is positive if real duration
   double *pp;           * is higher than the multiple of stepm and negative otherwise.
   double pos, k2, dateintsum=0,k2cpt=0;           */
   FILE *ficresp;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   char fileresp[FILENAMELENGTH];          if( s2 > nlstate){ 
              /* i.e. if s2 is a death state and if the date of death is known then the contribution
   pp=vector(1,nlstate);               to the likelihood is the probability to die between last step unit time and current 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);               step unit time, which is also the differences between probability to die before dh 
   strcpy(fileresp,"p");               and probability to die before dh-stepm . 
   strcat(fileresp,fileres);               In version up to 0.92 likelihood was computed
   if((ficresp=fopen(fileresp,"w"))==NULL) {          as if date of death was unknown. Death was treated as any other
     printf("Problem with prevalence resultfile: %s\n", fileresp);          health state: the date of the interview describes the actual state
     exit(0);          and not the date of a change in health state. The former idea was
   }          to consider that at each interview the state was recorded
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          (healthy, disable or death) and IMaCh was corrected; but when we
   j1=0;          introduced the exact date of death then we should have modified
            the contribution of an exact death to the likelihood. This new
   j=cptcoveff;          contribution is smaller and very dependent of the step unit
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          stepm. It is no more the probability to die between last interview
            and month of death but the probability to survive from last
   for(k1=1; k1<=j;k1++){          interview up to one month before death multiplied by the
     for(i1=1; i1<=ncodemax[k1];i1++){          probability to die within a month. Thanks to Chris
       j1++;          Jackson for correcting this bug.  Former versions increased
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          mortality artificially. The bad side is that we add another loop
         scanf("%d", i);*/          which slows down the processing. The difference can be up to 10%
       for (i=-1; i<=nlstate+ndeath; i++)            lower mortality.
         for (jk=-1; jk<=nlstate+ndeath; jk++)              */
           for(m=agemin; m <= agemax+3; m++)            lli=log(out[s1][s2] - savm[s1][s2]);
             freq[i][jk][m]=0;          }else{
                  lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       dateintsum=0;            /*  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 */
       k2cpt=0;          } 
       for (i=1; i<=imx; i++) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         bool=1;          /*if(lli ==000.0)*/
         if  (cptcovn>0) {          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
           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;
         }        } /* end of wave */
         if (bool==1) {      } /* end of individual */
           for(m=firstpass; m<=lastpass; m++){    }  else if(mle==2){
             k2=anint[m][i]+(mint[m][i]/12.);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
               if(agev[m][i]==0) agev[m][i]=agemax+1;        for(mi=1; mi<= wav[i]-1; mi++){
               if(agev[m][i]==1) agev[m][i]=agemax+2;          for (ii=1;ii<=nlstate+ndeath;ii++)
               if (m<lastpass) {            for (j=1;j<=nlstate+ndeath;j++){
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
               }            }
                        for(d=0; d<=dh[mi][i]; d++){
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {            newm=savm;
                 dateintsum=dateintsum+k2;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                 k2cpt++;            for (kk=1; kk<=cptcovage;kk++) {
               }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }            }
           }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
                    oldm=newm;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          } /* end mult */
         
       if  (cptcovn>0) {          s1=s[mw[mi][i]][i];
         fprintf(ficresp, "\n#********** Variable ");          s2=s[mw[mi+1][i]][i];
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          bbh=(double)bh[mi][i]/(double)stepm; 
         fprintf(ficresp, "**********\n#");          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       }          ipmx +=1;
       for(i=1; i<=nlstate;i++)          sw += weight[i];
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       fprintf(ficresp, "\n");        } /* end of wave */
            } /* end of individual */
       for(i=(int)agemin; i <= (int)agemax+3; i++){    }  else if(mle==3){  /* exponential inter-extrapolation */
         if(i==(int)agemax+3)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           printf("Total");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         else        for(mi=1; mi<= wav[i]-1; mi++){
           printf("Age %d", i);          for (ii=1;ii<=nlstate+ndeath;ii++)
         for(jk=1; jk <=nlstate ; jk++){            for (j=1;j<=nlstate+ndeath;j++){
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             pp[jk] += freq[jk][m][i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            }
         for(jk=1; jk <=nlstate ; jk++){          for(d=0; d<dh[mi][i]; d++){
           for(m=-1, pos=0; m <=0 ; m++)            newm=savm;
             pos += freq[jk][m][i];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           if(pp[jk]>=1.e-10)            for (kk=1; kk<=cptcovage;kk++) {
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           else            }
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
         for(jk=1; jk <=nlstate ; jk++){            oldm=newm;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          } /* end mult */
             pp[jk] += freq[jk][m][i];        
         }          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
         for(jk=1,pos=0; jk <=nlstate ; jk++)          bbh=(double)bh[mi][i]/(double)stepm; 
           pos += pp[jk];          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         for(jk=1; jk <=nlstate ; jk++){          ipmx +=1;
           if(pos>=1.e-5)          sw += weight[i];
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           else        } /* end of wave */
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      } /* end of individual */
           if( i <= (int) agemax){    }else if (mle==4){  /* ml=4 no inter-extrapolation */
             if(pos>=1.e-5){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
               probs[i][jk][j1]= pp[jk]/pos;        for(mi=1; mi<= wav[i]-1; mi++){
               /*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 (ii=1;ii<=nlstate+ndeath;ii++)
             }            for (j=1;j<=nlstate+ndeath;j++){
             else              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }            }
         }          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");          
         printf("\n");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
   }            oldm=newm;
   dateintmean=dateintsum/k2cpt;          } /* end mult */
          
   fclose(ficresp);          s1=s[mw[mi][i]][i];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          s2=s[mw[mi+1][i]][i];
   free_vector(pp,1,nlstate);          if( s2 > nlstate){ 
              lli=log(out[s1][s2] - savm[s1][s2]);
   /* End of Freq */          }else{
 }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }
 /************ Prevalence ********************/          ipmx +=1;
 void prevalence(int agemin, float 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)          sw += weight[i];
 {  /* Some frequencies */          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]); */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        } /* end of wave */
   double ***freq; /* Frequencies */      } /* end of individual */
   double *pp;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   double pos, k2;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   pp=vector(1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   j1=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
   j=cptcoveff;          for(d=0; d<dh[mi][i]; d++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for(k1=1; k1<=j;k1++){            for (kk=1; kk<=cptcovage;kk++) {
     for(i1=1; i1<=ncodemax[k1];i1++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       j1++;            }
                
       for (i=-1; i<=nlstate+ndeath; i++)              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for (jk=-1; jk<=nlstate+ndeath; jk++)                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           for(m=agemin; m <= agemax+3; m++)            savm=oldm;
             freq[i][jk][m]=0;            oldm=newm;
                } /* end mult */
       for (i=1; i<=imx; i++) {        
         bool=1;          s1=s[mw[mi][i]][i];
         if  (cptcovn>0) {          s2=s[mw[mi+1][i]][i];
           for (z1=1; z1<=cptcoveff; z1++)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          ipmx +=1;
               bool=0;          sw += weight[i];
         }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         if (bool==1) {          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
           for(m=firstpass; m<=lastpass; m++){        } /* end of wave */
             k2=anint[m][i]+(mint[m][i]/12.);      } /* end of individual */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    } /* End of if */
               if(agev[m][i]==0) agev[m][i]=agemax+1;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
               if(agev[m][i]==1) agev[m][i]=agemax+2;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
               if (m<lastpass) {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
                 if (calagedate>0)    return -l;
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];  }
                 else  
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  /*************** log-likelihood *************/
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];  double funcone( double *x)
               }  {
             }    /* Same as likeli but slower because of a lot of printf and if */
           }    int i, ii, j, k, mi, d, kk;
         }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       }    double **out;
       for(i=(int)agemin; i <= (int)agemax+3; i++){    double lli; /* Individual log likelihood */
         for(jk=1; jk <=nlstate ; jk++){    double llt;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    int s1, s2;
             pp[jk] += freq[jk][m][i];    double bbh, survp;
         }    /*extern weight */
         for(jk=1; jk <=nlstate ; jk++){    /* We are differentiating ll according to initial status */
           for(m=-1, pos=0; m <=0 ; m++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
             pos += freq[jk][m][i];    /*for(i=1;i<imx;i++) 
         }      printf(" %d\n",s[4][i]);
            */
         for(jk=1; jk <=nlstate ; jk++){    cov[1]=1.;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
             pp[jk] += freq[jk][m][i];    for(k=1; k<=nlstate; k++) ll[k]=0.;
         }  
            for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
              for(mi=1; mi<= wav[i]-1; mi++){
         for(jk=1; jk <=nlstate ; jk++){            for (ii=1;ii<=nlstate+ndeath;ii++)
           if( i <= (int) agemax){          for (j=1;j<=nlstate+ndeath;j++){
             if(pos>=1.e-5){            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               probs[i][jk][j1]= pp[jk]/pos;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }          }
           }        for(d=0; d<dh[mi][i]; d++){
         }          newm=savm;
                  cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }          for (kk=1; kk<=cptcovage;kk++) {
     }            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }          }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          savm=oldm;
   free_vector(pp,1,nlstate);          oldm=newm;
          } /* end mult */
 }  /* End of Freq */        
         s1=s[mw[mi][i]][i];
 /************* Waves Concatenation ***************/        s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm; 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        /* bias is positive if real duration
 {         * is higher than the multiple of stepm and negative otherwise.
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.         */
      Death is a valid wave (if date is known).        if( s2 > nlstate && (mle <5) ){  /* Jackson */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          lli=log(out[s1][s2] - savm[s1][s2]);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        } else if (mle==1){
      and mw[mi+1][i]. dh depends on stepm.          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
      */        } else if(mle==2){
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   int i, mi, m;        } else if(mle==3){  /* exponential inter-extrapolation */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-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 */
      double sum=0., jmean=0.;*/        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           lli=log(out[s1][s2]); /* Original formula */
   int j, k=0,jk, ju, jl;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   double sum=0.;          lli=log(out[s1][s2]); /* Original formula */
   jmin=1e+5;        } /* End of if */
   jmax=-1;        ipmx +=1;
   jmean=0.;        sw += weight[i];
   for(i=1; i<=imx; i++){        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     mi=0;  /*       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]); */
     m=firstpass;        if(globpr){
     while(s[m][i] <= nlstate){          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
       if(s[m][i]>=1)   %10.6f %10.6f %10.6f ", \
         mw[++mi][i]=m;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       if(m >=lastpass)                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         break;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       else            llt +=ll[k]*gipmx/gsw;
         m++;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     }/* end while */          }
     if (s[m][i] > nlstate){          fprintf(ficresilk," %10.6f\n", -llt);
       mi++;     /* Death is another wave */        }
       /* if(mi==0)  never been interviewed correctly before death */      } /* end of wave */
          /* Only death is a correct wave */    } /* end of individual */
       mw[mi][i]=m;    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 */
     wav[i]=mi;    if(globpr==0){ /* First time we count the contributions and weights */
     if(mi==0)      gipmx=ipmx;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      gsw=sw;
   }    }
     return -l;
   for(i=1; i<=imx; i++){  }
     for(mi=1; mi<wav[i];mi++){  
       if (stepm <=0)  
         dh[mi][i]=1;  /*************** function likelione ***********/
       else{  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         if (s[mw[mi+1][i]][i] > nlstate) {  {
           if (agedc[i] < 2*AGESUP) {    /* This routine should help understanding what is done with 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);       the selection of individuals/waves and
           if(j==0) j=1;  /* Survives at least one month after exam */       to check the exact contribution to the likelihood.
           k=k+1;       Plotting could be done.
           if (j >= jmax) jmax=j;     */
           if (j <= jmin) jmin=j;    int k;
           sum=sum+j;  
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    if(*globpri !=0){ /* Just counts and sums, no printings */
           }      strcpy(fileresilk,"ilk"); 
         }      strcat(fileresilk,fileres);
         else{      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        printf("Problem with resultfile: %s\n", fileresilk);
           k=k+1;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
           if (j >= jmax) jmax=j;      }
           else if (j <= jmin)jmin=j;      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");
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
           sum=sum+j;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
         }      for(k=1; k<=nlstate; k++) 
         jk= j/stepm;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
         jl= j -jk*stepm;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
         ju= j -(jk+1)*stepm;    }
         if(jl <= -ju)  
           dh[mi][i]=jk;    *fretone=(*funcone)(p);
         else    if(*globpri !=0){
           dh[mi][i]=jk+1;      fclose(ficresilk);
         if(dh[mi][i]==0)      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
           dh[mi][i]=1; /* At least one step */      fflush(fichtm); 
       }    } 
     }    return;
   }  }
   jmean=sum/k;  
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  
  }  /*********** Maximum Likelihood Estimation ***************/
 /*********** Tricode ****************************/  
 void tricode(int *Tvar, int **nbcode, int imx)  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 {  {
   int Ndum[20],ij=1, k, j, i;    int i,j, iter;
   int cptcode=0;    double **xi;
   cptcoveff=0;    double fret;
      double fretone; /* Only one call to likelihood */
   for (k=0; k<19; k++) Ndum[k]=0;    char filerespow[FILENAMELENGTH];
   for (k=1; k<=7; k++) ncodemax[k]=0;    xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      for (j=1;j<=npar;j++)
     for (i=1; i<=imx; i++) {        xi[i][j]=(i==j ? 1.0 : 0.0);
       ij=(int)(covar[Tvar[j]][i]);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       Ndum[ij]++;    strcpy(filerespow,"pow"); 
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    strcat(filerespow,fileres);
       if (ij > cptcode) cptcode=ij;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     }      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     for (i=0; i<=cptcode; i++) {    }
       if(Ndum[i]!=0) ncodemax[j]++;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     }    for (i=1;i<=nlstate;i++)
     ij=1;      for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fprintf(ficrespow,"\n");
     for (i=1; i<=ncodemax[j]; i++) {  
       for (k=0; k<=19; k++) {    powell(p,xi,npar,ftol,&iter,&fret,func);
         if (Ndum[k] != 0) {  
           nbcode[Tvar[j]][ij]=k;    fclose(ficrespow);
              printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
           ij++;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         }    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         if (ij > ncodemax[j]) break;  
       }    }
     }  
   }    /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
  for (k=0; k<19; k++) Ndum[k]=0;  {
     double  **a,**y,*x,pd;
  for (i=1; i<=ncovmodel-2; i++) {    double **hess;
       ij=Tvar[i];    int i, j,jk;
       Ndum[ij]++;    int *indx;
     }  
     double hessii(double p[], double delta, int theta, double delti[]);
  ij=1;    double hessij(double p[], double delti[], int i, int j);
  for (i=1; i<=10; i++) {    void lubksb(double **a, int npar, int *indx, double b[]) ;
    if((Ndum[i]!=0) && (i<=ncovcol)){    void ludcmp(double **a, int npar, int *indx, double *d) ;
      Tvaraff[ij]=i;  
      ij++;    hess=matrix(1,npar,1,npar);
    }  
  }    printf("\nCalculation of the hessian matrix. Wait...\n");
      fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     cptcoveff=ij-1;    for (i=1;i<=npar;i++){
 }      printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
 /*********** Health Expectancies ****************/      hess[i][i]=hessii(p,ftolhess,i,delti);
       /*printf(" %f ",p[i]);*/
 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 )      /*printf(" %lf ",hess[i][i]);*/
     }
 {    
   /* Health expectancies */    for (i=1;i<=npar;i++) {
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;      for (j=1;j<=npar;j++)  {
   double age, agelim, hf;        if (j>i) { 
   double ***p3mat,***varhe;          printf(".%d%d",i,j);fflush(stdout);
   double **dnewm,**doldm;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   double *xp;          hess[i][j]=hessij(p,delti,i,j);
   double **gp, **gm;          hess[j][i]=hess[i][j];    
   double ***gradg, ***trgradg;          /*printf(" %lf ",hess[i][j]);*/
   int theta;        }
       }
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    }
   xp=vector(1,npar);    printf("\n");
   dnewm=matrix(1,nlstate*2,1,npar);    fprintf(ficlog,"\n");
   doldm=matrix(1,nlstate*2,1,nlstate*2);  
      printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   fprintf(ficreseij,"# Health expectancies\n");    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   fprintf(ficreseij,"# Age");    
   for(i=1; i<=nlstate;i++)    a=matrix(1,npar,1,npar);
     for(j=1; j<=nlstate;j++)    y=matrix(1,npar,1,npar);
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    x=vector(1,npar);
   fprintf(ficreseij,"\n");    indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
   if(estepm < stepm){      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     printf ("Problem %d lower than %d\n",estepm, stepm);    ludcmp(a,npar,indx,&pd);
   }  
   else  hstepm=estepm;      for (j=1;j<=npar;j++) {
   /* We compute the life expectancy from trapezoids spaced every estepm months      for (i=1;i<=npar;i++) x[i]=0;
    * This is mainly to measure the difference between two models: for example      x[j]=1;
    * if stepm=24 months pijx are given only every 2 years and by summing them      lubksb(a,npar,indx,x);
    * we are calculating an estimate of the Life Expectancy assuming a linear      for (i=1;i<=npar;i++){ 
    * progression inbetween and thus overestimating or underestimating according        matcov[i][j]=x[i];
    * 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  
    * hypothesis. A more precise result, taking into account a more precise    printf("\n#Hessian matrix#\n");
    * curvature will be obtained if estepm is as small as stepm. */    fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
   /* For example we decided to compute the life expectancy with the smallest unit */      for (j=1;j<=npar;j++) { 
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        printf("%.3e ",hess[i][j]);
      nhstepm is the number of hstepm from age to agelim        fprintf(ficlog,"%.3e ",hess[i][j]);
      nstepm is the number of stepm from age to agelin.      }
      Look at hpijx to understand the reason of that which relies in memory size      printf("\n");
      and note for a fixed period like estepm months */      fprintf(ficlog,"\n");
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    }
      survival function given by stepm (the optimization length). Unfortunately it  
      means that if the survival funtion is printed only each two years of age and if    /* Recompute Inverse */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    for (i=1;i<=npar;i++)
      results. So we changed our mind and took the option of the best precision.      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   */    ludcmp(a,npar,indx,&pd);
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  
     /*  printf("\n#Hessian matrix recomputed#\n");
   agelim=AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    for (j=1;j<=npar;j++) {
     /* nhstepm age range expressed in number of stepm */      for (i=1;i<=npar;i++) x[i]=0;
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      x[j]=1;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */      lubksb(a,npar,indx,x);
     /* if (stepm >= YEARM) hstepm=1;*/      for (i=1;i<=npar;i++){ 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        y[i][j]=x[i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        printf("%.3e ",y[i][j]);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);        fprintf(ficlog,"%.3e ",y[i][j]);
     gp=matrix(0,nhstepm,1,nlstate*2);      }
     gm=matrix(0,nhstepm,1,nlstate*2);      printf("\n");
       fprintf(ficlog,"\n");
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    
      free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
     /* Computing Variances of health expectancies */    free_matrix(hess,1,npar,1,npar);
   
      for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){  }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }  /*************** hessian matrix ****************/
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    double hessii( double x[], double delta, int theta, double delti[])
    {
       cptj=0;    int i;
       for(j=1; j<= nlstate; j++){    int l=1, lmax=20;
         for(i=1; i<=nlstate; i++){    double k1,k2;
           cptj=cptj+1;    double p2[NPARMAX+1];
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    double res;
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           }    double fx;
         }    int k=0,kmax=10;
       }    double l1;
        
          fx=func(x);
       for(i=1; i<=npar; i++)    for (i=1;i<=npar;i++) p2[i]=x[i];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    for(l=0 ; l <=lmax; l++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        l1=pow(10,l);
            delts=delt;
       cptj=0;      for(k=1 ; k <kmax; k=k+1){
       for(j=1; j<= nlstate; j++){        delt = delta*(l1*k);
         for(i=1;i<=nlstate;i++){        p2[theta]=x[theta] +delt;
           cptj=cptj+1;        k1=func(p2)-fx;
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){        p2[theta]=x[theta]-delt;
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        k2=func(p2)-fx;
           }        /*res= (k1-2.0*fx+k2)/delt/delt; */
         }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       }        
       for(j=1; j<= nlstate*2; j++)  #ifdef DEBUG
         for(h=0; h<=nhstepm-1; h++){        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);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         }  #endif
      }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
            if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
 /* End theta */          k=kmax;
         }
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10.;
      for(h=0; h<=nhstepm-1; h++)        }
       for(j=1; j<=nlstate*2;j++)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         for(theta=1; theta <=npar; theta++)          delts=delt;
           trgradg[h][j][theta]=gradg[h][theta][j];        }
            }
     }
      for(i=1;i<=nlstate*2;i++)    delti[theta]=delts;
       for(j=1;j<=nlstate*2;j++)    return res; 
         varhe[i][j][(int)age] =0.;    
   }
      printf("%d|",(int)age);fflush(stdout);  
      for(h=0;h<=nhstepm-1;h++){  double hessij( double x[], double delti[], int thetai,int thetaj)
       for(k=0;k<=nhstepm-1;k++){  {
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    int i;
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);    int l=1, l1, lmax=20;
         for(i=1;i<=nlstate*2;i++)    double k1,k2,k3,k4,res,fx;
           for(j=1;j<=nlstate*2;j++)    double p2[NPARMAX+1];
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    int k;
       }  
     }    fx=func(x);
     /* Computing expectancies */    for (k=1; k<=2; k++) {
     for(i=1; i<=nlstate;i++)      for (i=1;i<=npar;i++) p2[i]=x[i];
       for(j=1; j<=nlstate;j++)      p2[thetai]=x[thetai]+delti[thetai]/k;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      k1=func(p2)-fx;
              
 /* 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]);*/      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         }      k2=func(p2)-fx;
     
     fprintf(ficreseij,"%3.0f",age );      p2[thetai]=x[thetai]-delti[thetai]/k;
     cptj=0;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     for(i=1; i<=nlstate;i++)      k3=func(p2)-fx;
       for(j=1; j<=nlstate;j++){    
         cptj++;      p2[thetai]=x[thetai]-delti[thetai]/k;
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       }      k4=func(p2)-fx;
     fprintf(ficreseij,"\n");      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
      #ifdef DEBUG
     free_matrix(gm,0,nhstepm,1,nlstate*2);      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     free_matrix(gp,0,nhstepm,1,nlstate*2);      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);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);  #endif
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);    }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    return res;
   }  }
   printf("\n");  
   /************** Inverse of matrix **************/
   free_vector(xp,1,npar);  void ludcmp(double **a, int n, int *indx, double *d) 
   free_matrix(dnewm,1,nlstate*2,1,npar);  { 
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);    int i,imax,j,k; 
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);    double big,dum,sum,temp; 
 }    double *vv; 
    
 /************ Variance ******************/    vv=vector(1,n); 
 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, int estepm)    *d=1.0; 
 {    for (i=1;i<=n;i++) { 
   /* Variance of health expectancies */      big=0.0; 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      for (j=1;j<=n;j++) 
   double **newm;        if ((temp=fabs(a[i][j])) > big) big=temp; 
   double **dnewm,**doldm;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   int i, j, nhstepm, hstepm, h, nstepm ;      vv[i]=1.0/big; 
   int k, cptcode;    } 
   double *xp;    for (j=1;j<=n;j++) { 
   double **gp, **gm;      for (i=1;i<j;i++) { 
   double ***gradg, ***trgradg;        sum=a[i][j]; 
   double ***p3mat;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   double age,agelim, hf;        a[i][j]=sum; 
   int theta;      } 
       big=0.0; 
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");      for (i=j;i<=n;i++) { 
   fprintf(ficresvij,"# Age");        sum=a[i][j]; 
   for(i=1; i<=nlstate;i++)        for (k=1;k<j;k++) 
     for(j=1; j<=nlstate;j++)          sum -= a[i][k]*a[k][j]; 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        a[i][j]=sum; 
   fprintf(ficresvij,"\n");        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
   xp=vector(1,npar);          imax=i; 
   dnewm=matrix(1,nlstate,1,npar);        } 
   doldm=matrix(1,nlstate,1,nlstate);      } 
        if (j != imax) { 
   if(estepm < stepm){        for (k=1;k<=n;k++) { 
     printf ("Problem %d lower than %d\n",estepm, stepm);          dum=a[imax][k]; 
   }          a[imax][k]=a[j][k]; 
   else  hstepm=estepm;            a[j][k]=dum; 
   /* 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.        *d = -(*d); 
      nhstepm is the number of hstepm from age to agelim        vv[imax]=vv[j]; 
      nstepm is the number of stepm from age to agelin.      } 
      Look at hpijx to understand the reason of that which relies in memory size      indx[j]=imax; 
      and note for a fixed period like k years */      if (a[j][j] == 0.0) a[j][j]=TINY; 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      if (j != n) { 
      survival function given by stepm (the optimization length). Unfortunately it        dum=1.0/(a[j][j]); 
      means that if the survival funtion is printed only each two years of age and if        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      } 
      results. So we changed our mind and took the option of the best precision.    } 
   */    free_vector(vv,1,n);  /* Doesn't work */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  ;
   agelim = AGESUP;  } 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  void lubksb(double **a, int n, int *indx, double b[]) 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  { 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int i,ii=0,ip,j; 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    double sum; 
     gp=matrix(0,nhstepm,1,nlstate);   
     gm=matrix(0,nhstepm,1,nlstate);    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
     for(theta=1; theta <=npar; theta++){      sum=b[ip]; 
       for(i=1; i<=npar; i++){ /* Computes gradient */      b[ip]=b[i]; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      if (ii) 
       }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        else if (sum) ii=i; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      b[i]=sum; 
     } 
       if (popbased==1) {    for (i=n;i>=1;i--) { 
         for(i=1; i<=nlstate;i++)      sum=b[i]; 
           prlim[i][i]=probs[(int)age][i][ij];      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       }      b[i]=sum/a[i][i]; 
      } 
       for(j=1; j<= nlstate; j++){  } 
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  /************ Frequencies ********************/
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  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 */
       }    
        int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       for(i=1; i<=npar; i++) /* Computes gradient */    int first;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double ***freq; /* Frequencies */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      double *pp, **prop;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
      FILE *ficresp;
       if (popbased==1) {    char fileresp[FILENAMELENGTH];
         for(i=1; i<=nlstate;i++)    
           prlim[i][i]=probs[(int)age][i][ij];    pp=vector(1,nlstate);
       }    prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
       for(j=1; j<= nlstate; j++){    strcat(fileresp,fileres);
         for(h=0; h<=nhstepm; h++){    if((ficresp=fopen(fileresp,"w"))==NULL) {
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      printf("Problem with prevalence resultfile: %s\n", fileresp);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
         }      exit(0);
       }    }
     freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
       for(j=1; j<= nlstate; j++)    j1=0;
         for(h=0; h<=nhstepm; h++){    
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    j=cptcoveff;
         }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     } /* End theta */  
     first=1;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  
     for(k1=1; k1<=j;k1++){
     for(h=0; h<=nhstepm; h++)      for(i1=1; i1<=ncodemax[k1];i1++){
       for(j=1; j<=nlstate;j++)        j1++;
         for(theta=1; theta <=npar; theta++)        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           trgradg[h][j][theta]=gradg[h][theta][j];          scanf("%d", i);*/
         for (i=-1; i<=nlstate+ndeath; i++)  
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     for(i=1;i<=nlstate;i++)            for(m=iagemin; m <= iagemax+3; m++)
       for(j=1;j<=nlstate;j++)              freq[i][jk][m]=0;
         vareij[i][j][(int)age] =0.;  
       for (i=1; i<=nlstate; i++)  
     for(h=0;h<=nhstepm;h++){        for(m=iagemin; m <= iagemax+3; m++)
       for(k=0;k<=nhstepm;k++){          prop[i][m]=0;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        dateintsum=0;
         for(i=1;i<=nlstate;i++)        k2cpt=0;
           for(j=1;j<=nlstate;j++)        for (i=1; i<=imx; i++) {
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          bool=1;
       }          if  (cptcovn>0) {
     }            for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     fprintf(ficresvij,"%.0f ",age );                bool=0;
     for(i=1; i<=nlstate;i++)          }
       for(j=1; j<=nlstate;j++){          if (bool==1){
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);            for(m=firstpass; m<=lastpass; m++){
       }              k2=anint[m][i]+(mint[m][i]/12.);
     fprintf(ficresvij,"\n");              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     free_matrix(gp,0,nhstepm,1,nlstate);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     free_matrix(gm,0,nhstepm,1,nlstate);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);                if (m<lastpass) {
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   } /* End age */                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                  }
   free_vector(xp,1,npar);                
   free_matrix(doldm,1,nlstate,1,npar);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   free_matrix(dnewm,1,nlstate,1,nlstate);                  dateintsum=dateintsum+k2;
                   k2cpt++;
 }                }
                 /*}*/
 /************ Variance of prevlim ******************/            }
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)          }
 {        }
   /* Variance of prevalence limit */         
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   double **newm;  
   double **dnewm,**doldm;        if  (cptcovn>0) {
   int i, j, nhstepm, hstepm;          fprintf(ficresp, "\n#********** Variable "); 
   int k, cptcode;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   double *xp;          fprintf(ficresp, "**********\n#");
   double *gp, *gm;        }
   double **gradg, **trgradg;        for(i=1; i<=nlstate;i++) 
   double age,agelim;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   int theta;        fprintf(ficresp, "\n");
            
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");        for(i=iagemin; i <= iagemax+3; i++){
   fprintf(ficresvpl,"# Age");          if(i==iagemax+3){
   for(i=1; i<=nlstate;i++)            fprintf(ficlog,"Total");
       fprintf(ficresvpl," %1d-%1d",i,i);          }else{
   fprintf(ficresvpl,"\n");            if(first==1){
               first=0;
   xp=vector(1,npar);              printf("See log file for details...\n");
   dnewm=matrix(1,nlstate,1,npar);            }
   doldm=matrix(1,nlstate,1,nlstate);            fprintf(ficlog,"Age %d", i);
            }
   hstepm=1*YEARM; /* Every year of age */          for(jk=1; jk <=nlstate ; jk++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   agelim = AGESUP;              pp[jk] += freq[jk][m][i]; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          for(jk=1; jk <=nlstate ; jk++){
     if (stepm >= YEARM) hstepm=1;            for(m=-1, pos=0; m <=0 ; m++)
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              pos += freq[jk][m][i];
     gradg=matrix(1,npar,1,nlstate);            if(pp[jk]>=1.e-10){
     gp=vector(1,nlstate);              if(first==1){
     gm=vector(1,nlstate);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               }
     for(theta=1; theta <=npar; theta++){              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       for(i=1; i<=npar; i++){ /* Computes gradient */            }else{
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              if(first==1)
       }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       for(i=1;i<=nlstate;i++)            }
         gp[i] = prlim[i][i];          }
      
       for(i=1; i<=npar; i++) /* Computes gradient */          for(jk=1; jk <=nlstate ; jk++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              pp[jk] += freq[jk][m][i];
       for(i=1;i<=nlstate;i++)          }       
         gm[i] = prlim[i][i];          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
       for(i=1;i<=nlstate;i++)            posprop += prop[jk][i];
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          }
     } /* End theta */          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
     trgradg =matrix(1,nlstate,1,npar);              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for(j=1; j<=nlstate;j++)              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       for(theta=1; theta <=npar; theta++)            }else{
         trgradg[j][theta]=gradg[theta][j];              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     for(i=1;i<=nlstate;i++)              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       varpl[i][(int)age] =0.;            }
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            if( i <= iagemax){
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);              if(pos>=1.e-5){
     for(i=1;i<=nlstate;i++)                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */                /*probs[i][jk][j1]= pp[jk]/pos;*/
                 /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     fprintf(ficresvpl,"%.0f ",age );              }
     for(i=1; i<=nlstate;i++)              else
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     fprintf(ficresvpl,"\n");            }
     free_vector(gp,1,nlstate);          }
     free_vector(gm,1,nlstate);          
     free_matrix(gradg,1,npar,1,nlstate);          for(jk=-1; jk <=nlstate+ndeath; jk++)
     free_matrix(trgradg,1,nlstate,1,npar);            for(m=-1; m <=nlstate+ndeath; m++)
   } /* End age */              if(freq[jk][m][i] !=0 ) {
               if(first==1)
   free_vector(xp,1,npar);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   free_matrix(doldm,1,nlstate,1,npar);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   free_matrix(dnewm,1,nlstate,1,nlstate);              }
           if(i <= iagemax)
 }            fprintf(ficresp,"\n");
           if(first==1)
 /************ Variance of one-step probabilities  ******************/            printf("Others in log...\n");
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)          fprintf(ficlog,"\n");
 {        }
   int i, j=0,  i1, k1, l1, t, tj;      }
   int k2, l2, j1,  z1;    }
   int k=0,l, cptcode;    dateintmean=dateintsum/k2cpt; 
   int first=1;   
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;    fclose(ficresp);
   double **dnewm,**doldm;    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
   double *xp;    free_vector(pp,1,nlstate);
   double *gp, *gm;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   double **gradg, **trgradg;    /* End of Freq */
   double **mu;  }
   double age,agelim, cov[NCOVMAX];  
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */  /************ Prevalence ********************/
   int theta;  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)
   char fileresprob[FILENAMELENGTH];  {  
   char fileresprobcov[FILENAMELENGTH];    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   char fileresprobcor[FILENAMELENGTH];       in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
   double ***varpij;    */
    
   strcpy(fileresprob,"prob");    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   strcat(fileresprob,fileres);    double ***freq; /* Frequencies */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    double *pp, **prop;
     printf("Problem with resultfile: %s\n", fileresprob);    double pos,posprop; 
   }    double  y2; /* in fractional years */
   strcpy(fileresprobcov,"probcov");    int iagemin, iagemax;
   strcat(fileresprobcov,fileres);  
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {    iagemin= (int) agemin;
     printf("Problem with resultfile: %s\n", fileresprobcov);    iagemax= (int) agemax;
   }    /*pp=vector(1,nlstate);*/
   strcpy(fileresprobcor,"probcor");    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   strcat(fileresprobcor,fileres);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    j1=0;
     printf("Problem with resultfile: %s\n", fileresprobcor);    
   }    j=cptcoveff;
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   printf("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);    for(k1=1; k1<=j;k1++){
        for(i1=1; i1<=ncodemax[k1];i1++){
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");        j1++;
   fprintf(ficresprob,"# Age");        
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");        for (i=1; i<=nlstate; i++)  
   fprintf(ficresprobcov,"# Age");          for(m=iagemin; m <= iagemax+3; m++)
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");            prop[i][m]=0.0;
   fprintf(ficresprobcov,"# Age");       
         for (i=1; i<=imx; i++) { /* Each individual */
           bool=1;
   for(i=1; i<=nlstate;i++)          if  (cptcovn>0) {
     for(j=1; j<=(nlstate+ndeath);j++){            for (z1=1; z1<=cptcoveff; z1++) 
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       fprintf(ficresprobcov," p%1d-%1d ",i,j);                bool=0;
       fprintf(ficresprobcor," p%1d-%1d ",i,j);          } 
     }            if (bool==1) { 
   fprintf(ficresprob,"\n");            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   fprintf(ficresprobcov,"\n");              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   fprintf(ficresprobcor,"\n");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   xp=vector(1,npar);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));                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); 
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);                  /*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]]);*/
   first=1;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {                  prop[s[m][i]][iagemax+3] += weight[i]; 
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);                } 
     exit(0);              }
   }            } /* end selection of waves */
   else{          }
     fprintf(ficgp,"\n# Routine varprob");        }
   }        for(i=iagemin; i <= iagemax+3; i++){  
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {          
     printf("Problem with html file: %s\n", optionfilehtm);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     exit(0);            posprop += prop[jk][i]; 
   }          } 
   else{  
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");          for(jk=1; jk <=nlstate ; jk++){     
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");            if( i <=  iagemax){ 
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");              if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
   }              } 
             } 
            }/* end jk */ 
   cov[1]=1;        }/* end i */ 
   tj=cptcoveff;      } /* end i1 */
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}    } /* end k1 */
   j1=0;    
   for(t=1; t<=tj;t++){    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     for(i1=1; i1<=ncodemax[t];i1++){    /*free_vector(pp,1,nlstate);*/
       j1++;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
        }  /* End of prevalence */
       if  (cptcovn>0) {  
         fprintf(ficresprob, "\n#********** Variable ");  /************* Waves Concatenation ***************/
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficresprob, "**********\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)
         fprintf(ficresprobcov, "\n#********** Variable ");  {
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         fprintf(ficresprobcov, "**********\n#");       Death is a valid wave (if date is known).
               mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         fprintf(ficgp, "\n#********** Variable ");       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);       and mw[mi+1][i]. dh depends on stepm.
         fprintf(ficgp, "**********\n#");       */
          
            int i, mi, m;
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);       double sum=0., jmean=0.;*/
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");    int first;
            int j, k=0,jk, ju, jl;
         fprintf(ficresprobcor, "\n#********** Variable ");        double sum=0.;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    first=0;
         fprintf(ficgp, "**********\n#");        jmin=1e+5;
       }    jmax=-1;
          jmean=0.;
       for (age=bage; age<=fage; age ++){    for(i=1; i<=imx; i++){
         cov[2]=age;      mi=0;
         for (k=1; k<=cptcovn;k++) {      m=firstpass;
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];      while(s[m][i] <= nlstate){
         }        if(s[m][i]>=1)
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          mw[++mi][i]=m;
         for (k=1; k<=cptcovprod;k++)        if(m >=lastpass)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          break;
                else
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));          m++;
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);      }/* end while */
         gp=vector(1,(nlstate)*(nlstate+ndeath));      if (s[m][i] > nlstate){
         gm=vector(1,(nlstate)*(nlstate+ndeath));        mi++;     /* Death is another wave */
            /* if(mi==0)  never been interviewed correctly before death */
         for(theta=1; theta <=npar; theta++){           /* Only death is a correct wave */
           for(i=1; i<=npar; i++)        mw[mi][i]=m;
             xp[i] = x[i] + (i==theta ?delti[theta]:0);      }
            
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      wav[i]=mi;
                if(mi==0){
           k=0;        nbwarn++;
           for(i=1; i<= (nlstate); i++){        if(first==0){
             for(j=1; j<=(nlstate+ndeath);j++){          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
               k=k+1;          first=1;
               gp[k]=pmmij[i][j];        }
             }        if(first==1){
           }          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
                  }
           for(i=1; i<=npar; i++)      } /* end mi==0 */
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    } /* End individuals */
      
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    for(i=1; i<=imx; i++){
           k=0;      for(mi=1; mi<wav[i];mi++){
           for(i=1; i<=(nlstate); i++){        if (stepm <=0)
             for(j=1; j<=(nlstate+ndeath);j++){          dh[mi][i]=1;
               k=k+1;        else{
               gm[k]=pmmij[i][j];          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             }            if (agedc[i] < 2*AGESUP) {
           }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                    if(j==0) j=1;  /* Survives at least one month after exam */
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)              else if(j<0){
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                  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]);
                 j=1; /* Temporary Dangerous patch */
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)                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);
           for(theta=1; theta <=npar; theta++)                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]);
             trgradg[j][theta]=gradg[theta][j];                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);
                      }
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);              k=k+1;
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);              if (j >= jmax) jmax=j;
                      if (j <= jmin) jmin=j;
         pmij(pmmij,cov,ncovmodel,x,nlstate);              sum=sum+j;
                      /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         k=0;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
         for(i=1; i<=(nlstate); i++){            }
           for(j=1; j<=(nlstate+ndeath);j++){          }
             k=k+1;          else{
             mu[k][(int) age]=pmmij[i][j];            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           }            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
         }            k=k+1;
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)            if (j >= jmax) jmax=j;
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)            else if (j <= jmin)jmin=j;
             varpij[i][j][(int)age] = doldm[i][j];            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*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]);*/
         /*printf("\n%d ",(int)age);            if(j<0){
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){              nberr++;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
      }*/              fprintf(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]);
             }
         fprintf(ficresprob,"\n%d ",(int)age);            sum=sum+j;
         fprintf(ficresprobcov,"\n%d ",(int)age);          }
         fprintf(ficresprobcor,"\n%d ",(int)age);          jk= j/stepm;
           jl= j -jk*stepm;
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)          ju= j -(jk+1)*stepm;
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){            if(jl==0){
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);              dh[mi][i]=jk;
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);              bh[mi][i]=0;
         }            }else{ /* We want a negative bias in order to only have interpolation ie
         i=0;                    * at the price of an extra matrix product in likelihood */
         for (k=1; k<=(nlstate);k++){              dh[mi][i]=jk+1;
           for (l=1; l<=(nlstate+ndeath);l++){              bh[mi][i]=ju;
             i=i++;            }
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);          }else{
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);            if(jl <= -ju){
             for (j=1; j<=i;j++){              dh[mi][i]=jk;
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);              bh[mi][i]=jl;       /* bias is positive if real duration
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));                                   * is higher than the multiple of stepm and negative otherwise.
             }                                   */
           }            }
         }/* end of loop for state */            else{
       } /* end of loop for age */              dh[mi][i]=jk+1;
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/              bh[mi][i]=ju;
       for (k1=1; k1<=(nlstate);k1++){            }
         for (l1=1; l1<=(nlstate+ndeath);l1++){            if(dh[mi][i]==0){
           if(l1==k1) continue;              dh[mi][i]=1; /* At least one step */
           i=(k1-1)*(nlstate+ndeath)+l1;              bh[mi][i]=ju; /* At least one step */
           for (k2=1; k2<=(nlstate);k2++){              /*  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);*/
             for (l2=1; l2<=(nlstate+ndeath);l2++){            }
               if(l2==k2) continue;          } /* end if mle */
               j=(k2-1)*(nlstate+ndeath)+l2;        }
               if(j<=i) continue;      } /* end wave */
               for (age=bage; age<=fage; age ++){    }
                 if ((int)age %5==0){    jmean=sum/k;
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;   }
                   mu1=mu[i][(int) age]/stepm*YEARM ;  
                   mu2=mu[j][(int) age]/stepm*YEARM;  /*********** Tricode ****************************/
                   /* Computing eigen value of matrix of covariance */  void tricode(int *Tvar, int **nbcode, int imx)
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));  {
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));    
                   printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);    int Ndum[20],ij=1, k, j, i, maxncov=19;
                   /* Eigen vectors */    int cptcode=0;
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));    cptcoveff=0; 
                   v21=sqrt(1.-v11*v11);   
                   v12=-v21;    for (k=0; k<maxncov; k++) Ndum[k]=0;
                   v22=v11;    for (k=1; k<=7; k++) ncodemax[k]=0;
                   /*printf(fignu*/  
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                   if(first==1){                                 modality*/ 
                     first=0;        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
                     fprintf(ficgp,"\nset parametric;set nolabel");        Ndum[ij]++; /*store the modality */
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);                                         Tvar[j]. If V=sex and male is 0 and 
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);                                         female is 1, then  cptcode=1.*/
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);      }
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);  
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);      for (i=0; i<=cptcode; i++) {
                     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)) t \"%d\"",\        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 */
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \      }
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);  
                   }else{      ij=1; 
                     first=0;      for (i=1; i<=ncodemax[j]; i++) {
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);        for (k=0; k<= maxncov; k++) {
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);          if (Ndum[k] != 0) {
                     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)) t \"%d\"",\            nbcode[Tvar[j]][ij]=k; 
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \            /* 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; */
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);            
                   }/* if first */            ij++;
                 } /* age mod 5 */          }
               } /* end loop age */          if (ij > ncodemax[j]) break; 
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);        }  
               first=1;      } 
             } /*l12 */    }  
           } /* k12 */  
         } /*l1 */   for (k=0; k< maxncov; k++) Ndum[k]=0;
       }/* k1 */  
     } /* loop covariates */   for (i=1; i<=ncovmodel-2; i++) { 
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));     ij=Tvar[i];
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));     Ndum[ij]++;
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);   }
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);   ij=1;
   }   for (i=1; i<= maxncov; i++) {
   free_vector(xp,1,npar);     if((Ndum[i]!=0) && (i<=ncovcol)){
   fclose(ficresprob);       Tvaraff[ij]=i; /*For printing */
   fclose(ficresprobcov);       ij++;
   fclose(ficresprobcor);     }
   fclose(ficgp);   }
   fclose(fichtm);   
 }   cptcoveff=ij-1; /*Number of simple covariates*/
   }
   
 /******************* Printing html file ***********/  /*********** Health Expectancies ****************/
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \  
                   int lastpass, int stepm, int weightopt, char model[],\  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 )
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\  
                   int popforecast, int estepm ,\  {
                   double jprev1, double mprev1,double anprev1, \    /* Health expectancies */
                   double jprev2, double mprev2,double anprev2){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   int jj1, k1, i1, cpt;    double age, agelim, hf;
   /*char optionfilehtm[FILENAMELENGTH];*/    double ***p3mat,***varhe;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {    double **dnewm,**doldm;
     printf("Problem with %s \n",optionfilehtm), exit(0);    double *xp;
   }    double **gp, **gm;
     double ***gradg, ***trgradg;
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n    int theta;
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n  
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n    xp=vector(1,npar);
  - Life expectancies by age and initial health status (estepm=%2d months):    dnewm=matrix(1,nlstate*nlstate,1,npar);
    <a href=\"e%s\">e%s</a> <br>\n</li>", \    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    
     fprintf(ficreseij,"# Health expectancies\n");
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n    fprintf(ficreseij,"# Age");
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n    for(i=1; i<=nlstate;i++)
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n      for(j=1; j<=nlstate;j++)
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n        fprintf(ficreseij," %1d-%1d (SE)",i,j);
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n    fprintf(ficreseij,"\n");
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n  
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    if(estepm < stepm){
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
  if(popforecast==1) fprintf(fichtm,"\n    else  hstepm=estepm;   
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    /* We compute the life expectancy from trapezoids spaced every estepm months
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n     * This is mainly to measure the difference between two models: for example
         <br>",fileres,fileres,fileres,fileres);     * if stepm=24 months pijx are given only every 2 years and by summing them
  else     * we are calculating an estimate of the Life Expectancy assuming a linear 
    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);     * progression in between and thus overestimating or underestimating according
 fprintf(fichtm," <li><b>Graphs</b></li><p>");     * 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
  m=cptcoveff;     * to compare the new estimate of Life expectancy with the same linear 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}     * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
  jj1=0;  
  for(k1=1; k1<=m;k1++){    /* For example we decided to compute the life expectancy with the smallest unit */
    for(i1=1; i1<=ncodemax[k1];i1++){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      jj1++;       nhstepm is the number of hstepm from age to agelim 
      if (cptcovn > 0) {       nstepm is the number of stepm from age to agelin. 
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");       Look at hpijx to understand the reason of that which relies in memory size
        for (cpt=1; cpt<=cptcoveff;cpt++)       and note for a fixed period like estepm months */
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");       survival function given by stepm (the optimization length). Unfortunately it
      }       means that if the survival funtion is printed only each two years of age and if
      /* Pij */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>       results. So we changed our mind and took the option of the best precision.
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        */
      /* Quasi-incidences */    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>  
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    agelim=AGESUP;
        /* Stable prevalence in each health state */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        for(cpt=1; cpt<nlstate;cpt++){      /* nhstepm age range expressed in number of stepm */
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        }      /* if (stepm >= YEARM) hstepm=1;*/
     for(cpt=1; cpt<=nlstate;cpt++) {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 interval) in state (%d): v%s%d%d.png <br>      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        gp=matrix(0,nhstepm,1,nlstate*nlstate);
      }      gm=matrix(0,nhstepm,1,nlstate*nlstate);
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>      /* Computed by stepm unit matrices, product of hstepm matrices, stored
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
      }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and   
 health expectancies in states (1) and (2): e%s%d.png<br>  
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    }  
  }      /* Computing Variances of health expectancies */
 fclose(fichtm);  
 }       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
 /******************* Gnuplot file **************/          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    
   int ng;        cptj=0;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {        for(j=1; j<= nlstate; j++){
     printf("Problem with file %s",optionfilegnuplot);          for(i=1; i<=nlstate; i++){
   }            cptj=cptj+1;
             for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
 #ifdef windows              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     fprintf(ficgp,"cd \"%s\" \n",pathc);            }
 #endif          }
 m=pow(2,cptcoveff);        }
         
  /* 1eme*/       
   for (cpt=1; cpt<= nlstate ; cpt ++) {        for(i=1; i<=npar; i++) 
    for (k1=1; k1<= m ; k1 ++) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 #ifdef windows        
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        cptj=0;
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);        for(j=1; j<= nlstate; j++){
 #endif          for(i=1;i<=nlstate;i++){
 #ifdef unix            cptj=cptj+1;
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);  
 #endif              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
 for (i=1; i<= nlstate ; i ++) {          }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=1; j<= nlstate*nlstate; j++)
 }          for(h=0; h<=nhstepm-1; h++){
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     for (i=1; i<= nlstate ; i ++) {          }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");       } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");     
 }  /* End theta */
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  
      for (i=1; i<= nlstate ; i ++) {       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");       for(h=0; h<=nhstepm-1; h++)
 }          for(j=1; j<=nlstate*nlstate;j++)
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          for(theta=1; theta <=npar; theta++)
 #ifdef unix            trgradg[h][j][theta]=gradg[h][theta][j];
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");       
 #endif  
    }       for(i=1;i<=nlstate*nlstate;i++)
   }        for(j=1;j<=nlstate*nlstate;j++)
   /*2 eme*/          varhe[i][j][(int)age] =0.;
   
   for (k1=1; k1<= m ; k1 ++) {       printf("%d|",(int)age);fflush(stdout);
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);       for(h=0;h<=nhstepm-1;h++){
            for(k=0;k<=nhstepm-1;k++){
     for (i=1; i<= nlstate+1 ; i ++) {          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       k=2*i;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          for(i=1;i<=nlstate*nlstate;i++)
       for (j=1; j<= nlstate+1 ; j ++) {            for(j=1;j<=nlstate*nlstate;j++)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }        }
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      /* Computing expectancies */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      for(i=1; i<=nlstate;i++)
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        for(j=1; j<=nlstate;j++)
       for (j=1; j<= nlstate+1 ; j ++) {          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
         else fprintf(ficgp," \%%*lf (\%%*lf)");            
 }    /* 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]);*/
       fprintf(ficgp,"\" t\"\" w l 0,");  
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          }
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      fprintf(ficreseij,"%3.0f",age );
   else fprintf(ficgp," \%%*lf (\%%*lf)");      cptj=0;
 }        for(i=1; i<=nlstate;i++)
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        for(j=1; j<=nlstate;j++){
       else fprintf(ficgp,"\" t\"\" w l 0,");          cptj++;
     }          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   }        }
        fprintf(ficreseij,"\n");
   /*3eme*/     
       free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   for (k1=1; k1<= m ; k1 ++) {      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     for (cpt=1; cpt<= nlstate ; cpt ++) {      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
       k=2+nlstate*(2*cpt-2);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    }
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    printf("\n");
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    fprintf(ficlog,"\n");
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    free_vector(xp,1,npar);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
 */  }
       for (i=1; i< nlstate ; i ++) {  
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);  /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
       }  {
     }    /* Variance of health expectancies */
   }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
      /* double **newm;*/
   /* CV preval stat */    double **dnewm,**doldm;
     for (k1=1; k1<= m ; k1 ++) {    double **dnewmp,**doldmp;
     for (cpt=1; cpt<nlstate ; cpt ++) {    int i, j, nhstepm, hstepm, h, nstepm ;
       k=3;    int k, cptcode;
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    double *xp;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
       for (i=1; i< nlstate ; i ++)    double **gradgp, **trgradgp; /* for var p point j */
         fprintf(ficgp,"+$%d",k+i+1);    double *gpp, *gmp; /* for var p point j */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
          double ***p3mat;
       l=3+(nlstate+ndeath)*cpt;    double age,agelim, hf;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    double ***mobaverage;
       for (i=1; i< nlstate ; i ++) {    int theta;
         l=3+(nlstate+ndeath)*cpt;    char digit[4];
         fprintf(ficgp,"+$%d",l+i+1);    char digitp[25];
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      char fileresprobmorprev[FILENAMELENGTH];
     }  
   }      if(popbased==1){
        if(mobilav!=0)
   /* proba elementaires */        strcpy(digitp,"-populbased-mobilav-");
    for(i=1,jk=1; i <=nlstate; i++){      else strcpy(digitp,"-populbased-nomobil-");
     for(k=1; k <=(nlstate+ndeath); k++){    }
       if (k != i) {    else 
         for(j=1; j <=ncovmodel; j++){      strcpy(digitp,"-stablbased-");
          
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    if (mobilav!=0) {
           jk++;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           fprintf(ficgp,"\n");      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(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/    strcpy(fileresprobmorprev,"prmorprev"); 
      for(jk=1; jk <=m; jk++) {    sprintf(digit,"%-d",ij);
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
        if (ng==2)    strcat(fileresprobmorprev,digit); /* Tvar to be done */
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
        else    strcat(fileresprobmorprev,fileres);
          fprintf(ficgp,"\nset title \"Probability\"\n");    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
        i=1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
        for(k2=1; k2<=nlstate; k2++) {    }
          k3=i;    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
          for(k=1; k<=(nlstate+ndeath); k++) {    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
            if (k != k2){    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);
              if(ng==2)    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
              else      fprintf(ficresprobmorprev," p.%-d SE",j);
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      for(i=1; i<=nlstate;i++)
              ij=1;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
              for(j=3; j <=ncovmodel; j++) {    }  
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    fprintf(ficresprobmorprev,"\n");
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    fprintf(ficgp,"\n# Routine varevsij");
                  ij++;    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
                }    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
                else  /*   } */
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
              }  
              fprintf(ficgp,")/(1");    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
                  fprintf(ficresvij,"# Age");
              for(k1=1; k1 <=nlstate; k1++){      for(i=1; i<=nlstate;i++)
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      for(j=1; j<=nlstate;j++)
                ij=1;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
                for(j=3; j <=ncovmodel; j++){    fprintf(ficresvij,"\n");
                  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]]]);    xp=vector(1,npar);
                    ij++;    dnewm=matrix(1,nlstate,1,npar);
                  }    doldm=matrix(1,nlstate,1,nlstate);
                  else    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                }  
                fprintf(ficgp,")");    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
              }    gpp=vector(nlstate+1,nlstate+ndeath);
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);    gmp=vector(nlstate+1,nlstate+ndeath);
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
              i=i+ncovmodel;    
            }    if(estepm < stepm){
          }      printf ("Problem %d lower than %d\n",estepm, stepm);
        }    }
      }    else  hstepm=estepm;   
    }    /* For example we decided to compute the life expectancy with the smallest unit */
    fclose(ficgp);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 }  /* end gnuplot */       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
 /*************** Moving average **************/       and note for a fixed period like k years */
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
   int i, cpt, cptcod;       means that if the survival funtion is printed every two years of age and if
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       for (i=1; i<=nlstate;i++)       results. So we changed our mind and took the option of the best precision.
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    */
           mobaverage[(int)agedeb][i][cptcod]=0.;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
        agelim = AGESUP;
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       for (i=1; i<=nlstate;i++){      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           for (cpt=0;cpt<=4;cpt++){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
           }      gp=matrix(0,nhstepm,1,nlstate);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;      gm=matrix(0,nhstepm,1,nlstate);
         }  
       }  
     }      for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
 }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 /************** Forecasting ******************/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){  
          if (popbased==1) {
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          if(mobilav ==0){
   int *popage;            for(i=1; i<=nlstate;i++)
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;              prlim[i][i]=probs[(int)age][i][ij];
   double *popeffectif,*popcount;          }else{ /* mobilav */ 
   double ***p3mat;            for(i=1; i<=nlstate;i++)
   char fileresf[FILENAMELENGTH];              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
  agelim=AGESUP;        }
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    
         for(j=1; j<= nlstate; j++){
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          for(h=0; h<=nhstepm; h++){
              for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   strcpy(fileresf,"f");          }
   strcat(fileresf,fileres);        }
   if((ficresf=fopen(fileresf,"w"))==NULL) {        /* This for computing probability of death (h=1 means
     printf("Problem with forecast resultfile: %s\n", fileresf);           computed over hstepm matrices product = hstepm*stepm months) 
   }           as a weighted average of prlim.
   printf("Computing forecasting: result on file '%s' \n", fileresf);        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
   if (mobilav==1) {        }    
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        /* end probability of death */
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
   stepsize=(int) (stepm+YEARM-1)/YEARM;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   if (stepm<=12) stepsize=1;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     
   agelim=AGESUP;        if (popbased==1) {
            if(mobilav ==0){
   hstepm=1;            for(i=1; i<=nlstate;i++)
   hstepm=hstepm/stepm;              prlim[i][i]=probs[(int)age][i][ij];
   yp1=modf(dateintmean,&yp);          }else{ /* mobilav */ 
   anprojmean=yp;            for(i=1; i<=nlstate;i++)
   yp2=modf((yp1*12),&yp);              prlim[i][i]=mobaverage[(int)age][i][ij];
   mprojmean=yp;          }
   yp1=modf((yp2*30.5),&yp);        }
   jprojmean=yp;  
   if(jprojmean==0) jprojmean=1;        for(j=1; j<= nlstate; j++){
   if(mprojmean==0) jprojmean=1;          for(h=0; h<=nhstepm; h++){
              for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
            }
   for(cptcov=1;cptcov<=i2;cptcov++){        }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        /* This for computing probability of death (h=1 means
       k=k+1;           computed over hstepm matrices product = hstepm*stepm months) 
       fprintf(ficresf,"\n#******");           as a weighted average of prlim.
       for(j=1;j<=cptcoveff;j++) {        */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
       fprintf(ficresf,"******\n");           gmp[j] += prlim[i][i]*p3mat[i][j][1];
       fprintf(ficresf,"# StartingAge FinalAge");        }    
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        /* end probability of death */
        
              for(j=1; j<= nlstate; j++) /* vareij */
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {          for(h=0; h<=nhstepm; h++){
         fprintf(ficresf,"\n");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            }
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
           nhstepm = nhstepm/hstepm;        }
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } /* End theta */
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
          
           for (h=0; h<=nhstepm; h++){      for(h=0; h<=nhstepm; h++) /* veij */
             if (h==(int) (calagedate+YEARM*cpt)) {        for(j=1; j<=nlstate;j++)
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);          for(theta=1; theta <=npar; theta++)
             }            trgradg[h][j][theta]=gradg[h][theta][j];
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
               for(i=1; i<=nlstate;i++) {                      for(theta=1; theta <=npar; theta++)
                 if (mobilav==1)          trgradgp[j][theta]=gradgp[theta][j];
                   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];      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                 }      for(i=1;i<=nlstate;i++)
                        for(j=1;j<=nlstate;j++)
               }          vareij[i][j][(int)age] =0.;
               if (h==(int)(calagedate+12*cpt)){  
                 fprintf(ficresf," %.3f", kk1);      for(h=0;h<=nhstepm;h++){
                                for(k=0;k<=nhstepm;k++){
               }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
             }          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           }          for(i=1;i<=nlstate;i++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(j=1;j<=nlstate;j++)
         }              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       }        }
     }      }
   }    
              /* pptj */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      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);
   fclose(ficresf);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
 }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
 /************** Forecasting ******************/          varppt[j][i]=doldmp[j][i];
 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){      /* end ppptj */
        /*  x centered again */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   int *popage;      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;   
   double *popeffectif,*popcount;      if (popbased==1) {
   double ***p3mat,***tabpop,***tabpopprev;        if(mobilav ==0){
   char filerespop[FILENAMELENGTH];          for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }else{ /* mobilav */ 
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(i=1; i<=nlstate;i++)
   agelim=AGESUP;            prlim[i][i]=mobaverage[(int)age][i][ij];
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;        }
        }
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);               
        /* This for computing probability of death (h=1 means
           computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   strcpy(filerespop,"pop");         as a weighted average of prlim.
   strcat(filerespop,fileres);      */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      for(j=nlstate+1;j<=nlstate+ndeath;j++){
     printf("Problem with forecast resultfile: %s\n", filerespop);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   }          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   printf("Computing forecasting: result on file '%s' \n", filerespop);      }    
       /* end probability of death */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   if (mobilav==1) {      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     movingaverage(agedeb, fage, ageminpar, mobaverage);        for(i=1; i<=nlstate;i++){
   }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
   stepsize=(int) (stepm+YEARM-1)/YEARM;      } 
   if (stepm<=12) stepsize=1;      fprintf(ficresprobmorprev,"\n");
    
   agelim=AGESUP;      fprintf(ficresvij,"%.0f ",age );
        for(i=1; i<=nlstate;i++)
   hstepm=1;        for(j=1; j<=nlstate;j++){
   hstepm=hstepm/stepm;          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
          }
   if (popforecast==1) {      fprintf(ficresvij,"\n");
     if((ficpop=fopen(popfile,"r"))==NULL) {      free_matrix(gp,0,nhstepm,1,nlstate);
       printf("Problem with population file : %s\n",popfile);exit(0);      free_matrix(gm,0,nhstepm,1,nlstate);
     }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     popage=ivector(0,AGESUP);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     popeffectif=vector(0,AGESUP);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     popcount=vector(0,AGESUP);    } /* End age */
        free_vector(gpp,nlstate+1,nlstate+ndeath);
     i=1;      free_vector(gmp,nlstate+1,nlstate+ndeath);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
        free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     imx=i;    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   }    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   for(cptcov=1;cptcov<=i2;cptcov++){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
       k=k+1;    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
       fprintf(ficrespop,"\n#******");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
       for(j=1;j<=cptcoveff;j++) {    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
       }    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
       fprintf(ficrespop,"******\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);
       fprintf(ficrespop,"# Age");  */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
       if (popforecast==1)  fprintf(ficrespop," [Population]");    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
        
       for (cpt=0; cpt<=0;cpt++) {    free_vector(xp,1,npar);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      free_matrix(doldm,1,nlstate,1,nlstate);
            free_matrix(dnewm,1,nlstate,1,npar);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
           nhstepm = nhstepm/hstepm;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
              if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fclose(ficresprobmorprev);
           oldm=oldms;savm=savms;    fflush(ficgp);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fflush(fichtm); 
          }  /* end varevsij */
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {  /************ Variance of prevlim ******************/
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  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(j=1; j<=nlstate+ndeath;j++) {    /* Variance of prevalence limit */
               kk1=0.;kk2=0;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
               for(i=1; i<=nlstate;i++) {                  double **newm;
                 if (mobilav==1)    double **dnewm,**doldm;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    int i, j, nhstepm, hstepm;
                 else {    int k, cptcode;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    double *xp;
                 }    double *gp, *gm;
               }    double **gradg, **trgradg;
               if (h==(int)(calagedate+12*cpt)){    double age,agelim;
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    int theta;
                   /*fprintf(ficrespop," %.3f", kk1);     
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
               }    fprintf(ficresvpl,"# Age");
             }    for(i=1; i<=nlstate;i++)
             for(i=1; i<=nlstate;i++){        fprintf(ficresvpl," %1d-%1d",i,i);
               kk1=0.;    fprintf(ficresvpl,"\n");
                 for(j=1; j<=nlstate;j++){  
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    xp=vector(1,npar);
                 }    dnewm=matrix(1,nlstate,1,npar);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    doldm=matrix(1,nlstate,1,nlstate);
             }    
     hstepm=1*YEARM; /* Every year of age */
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    agelim = AGESUP;
           }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         }      if (stepm >= YEARM) hstepm=1;
       }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
        gradg=matrix(1,npar,1,nlstate);
   /******/      gp=vector(1,nlstate);
       gm=vector(1,nlstate);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        for(theta=1; theta <=npar; theta++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        for(i=1; i<=npar; i++){ /* Computes gradient */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           nhstepm = nhstepm/hstepm;        }
                  prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(i=1;i<=nlstate;i++)
           oldm=oldms;savm=savms;          gp[i] = prlim[i][i];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        
           for (h=0; h<=nhstepm; h++){        for(i=1; i<=npar; i++) /* Computes gradient */
             if (h==(int) (calagedate+YEARM*cpt)) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             }        for(i=1;i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++) {          gm[i] = prlim[i][i];
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                      for(i=1;i<=nlstate;i++)
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
               }      } /* End theta */
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  
             }      trgradg =matrix(1,nlstate,1,npar);
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(j=1; j<=nlstate;j++)
         }        for(theta=1; theta <=npar; theta++)
       }          trgradg[j][theta]=gradg[theta][j];
    }  
   }      for(i=1;i<=nlstate;i++)
          varpl[i][(int)age] =0.;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   if (popforecast==1) {      for(i=1;i<=nlstate;i++)
     free_ivector(popage,0,AGESUP);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     free_vector(popeffectif,0,AGESUP);  
     free_vector(popcount,0,AGESUP);      fprintf(ficresvpl,"%.0f ",age );
   }      for(i=1; i<=nlstate;i++)
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(ficresvpl,"\n");
   fclose(ficrespop);      free_vector(gp,1,nlstate);
 }      free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
 /***********************************************/      free_matrix(trgradg,1,nlstate,1,npar);
 /**************** Main Program *****************/    } /* End age */
 /***********************************************/  
     free_vector(xp,1,npar);
 int main(int argc, char *argv[])    free_matrix(doldm,1,nlstate,1,npar);
 {    free_matrix(dnewm,1,nlstate,1,nlstate);
   
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  }
   double agedeb, agefin,hf;  
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;  /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   double fret;  {
   double **xi,tmp,delta;    int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
   double dum; /* Dummy variable */    int k=0,l, cptcode;
   double ***p3mat;    int first=1, first1;
   int *indx;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   char line[MAXLINE], linepar[MAXLINE];    double **dnewm,**doldm;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    double *xp;
   int firstobs=1, lastobs=10;    double *gp, *gm;
   int sdeb, sfin; /* Status at beginning and end */    double **gradg, **trgradg;
   int c,  h , cpt,l;    double **mu;
   int ju,jl, mi;    double age,agelim, cov[NCOVMAX];
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    int theta;
   int mobilav=0,popforecast=0;    char fileresprob[FILENAMELENGTH];
   int hstepm, nhstepm;    char fileresprobcov[FILENAMELENGTH];
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    char fileresprobcor[FILENAMELENGTH];
   
   double bage, fage, age, agelim, agebase;    double ***varpij;
   double ftolpl=FTOL;  
   double **prlim;    strcpy(fileresprob,"prob"); 
   double *severity;    strcat(fileresprob,fileres);
   double ***param; /* Matrix of parameters */    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   double  *p;      printf("Problem with resultfile: %s\n", fileresprob);
   double **matcov; /* Matrix of covariance */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   double ***delti3; /* Scale */    }
   double *delti; /* Scale */    strcpy(fileresprobcov,"probcov"); 
   double ***eij, ***vareij;    strcat(fileresprobcov,fileres);
   double **varpl; /* Variances of prevalence limits by age */    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   double *epj, vepp;      printf("Problem with resultfile: %s\n", fileresprobcov);
   double kk1, kk2;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    }
      strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
   char *alph[]={"a","a","b","c","d","e"}, str[4];    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   char z[1]="c", occ;    }
 #include <sys/time.h>    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
 #include <time.h>    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   /* long total_usecs;    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   struct timeval start_time, end_time;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   getcwd(pathcd, size);    fprintf(ficresprob,"# Age");
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   printf("\n%s",version);    fprintf(ficresprobcov,"# Age");
   if(argc <=1){    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     printf("\nEnter the parameter file name: ");    fprintf(ficresprobcov,"# Age");
     scanf("%s",pathtot);  
   }  
   else{    for(i=1; i<=nlstate;i++)
     strcpy(pathtot,argv[1]);      for(j=1; j<=(nlstate+ndeath);j++){
   }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   /*cygwin_split_path(pathtot,path,optionfile);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      }  
   /* cutv(path,optionfile,pathtot,'\\');*/   /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    fprintf(ficresprobcor,"\n");
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);   */
   chdir(path);   xp=vector(1,npar);
   replace(pathc,path);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
 /*-------- arguments in the command line --------*/    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   strcpy(fileres,"r");    first=1;
   strcat(fileres, optionfilefiname);    fprintf(ficgp,"\n# Routine varprob");
   strcat(fileres,".txt");    /* Other files have txt extension */    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   /*---------arguments file --------*/  
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
     printf("Problem with optionfile %s\n",optionfile);    file %s<br>\n",optionfilehtmcov);
     goto end;    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");
   strcpy(filereso,"o");    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. \
   strcat(filereso,fileres);  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   if((ficparo=fopen(filereso,"w"))==NULL) {  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  standard deviations wide on each axis. <br>\
   }   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   /* Reads comments: lines beginning with '#' */  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    cov[1]=1;
     fgets(line, MAXLINE, ficpar);    tj=cptcoveff;
     puts(line);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     fputs(line,ficparo);    j1=0;
   }    for(t=1; t<=tj;t++){
   ungetc(c,ficpar);      for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
   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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);        if  (cptcovn>0) {
   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(ficresprob, "\n#********** Variable "); 
   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);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresprob, "**********\n#\n");
     ungetc(c,ficpar);          fprintf(ficresprobcov, "\n#********** Variable "); 
     fgets(line, MAXLINE, ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     puts(line);          fprintf(ficresprobcov, "**********\n#\n");
     fputs(line,ficparo);          
   }          fprintf(ficgp, "\n#********** Variable "); 
   ungetc(c,ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficgp, "**********\n#\n");
              
   covar=matrix(0,NCOVMAX,1,n);          
   cptcovn=0;          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   ncovmodel=2+cptcovn;          
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */          fprintf(ficresprobcor, "\n#********** Variable ");    
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /* Read guess parameters */          fprintf(ficresprobcor, "**********\n#");    
   /* Reads comments: lines beginning with '#' */        }
   while((c=getc(ficpar))=='#' && c!= EOF){        
     ungetc(c,ficpar);        for (age=bage; age<=fage; age ++){ 
     fgets(line, MAXLINE, ficpar);          cov[2]=age;
     puts(line);          for (k=1; k<=cptcovn;k++) {
     fputs(line,ficparo);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   }          }
   ungetc(c,ficpar);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
            for (k=1; k<=cptcovprod;k++)
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     for(i=1; i <=nlstate; i++)          
     for(j=1; j <=nlstate+ndeath-1; j++){          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       fscanf(ficpar,"%1d%1d",&i1,&j1);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       fprintf(ficparo,"%1d%1d",i1,j1);          gp=vector(1,(nlstate)*(nlstate+ndeath));
       printf("%1d%1d",i,j);          gm=vector(1,(nlstate)*(nlstate+ndeath));
       for(k=1; k<=ncovmodel;k++){      
         fscanf(ficpar," %lf",&param[i][j][k]);          for(theta=1; theta <=npar; theta++){
         printf(" %lf",param[i][j][k]);            for(i=1; i<=npar; i++)
         fprintf(ficparo," %lf",param[i][j][k]);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       }            
       fscanf(ficpar,"\n");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       printf("\n");            
       fprintf(ficparo,"\n");            k=0;
     }            for(i=1; i<= (nlstate); i++){
                for(j=1; j<=(nlstate+ndeath);j++){
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;                k=k+1;
                 gp[k]=pmmij[i][j];
   p=param[1][1];              }
              }
   /* Reads comments: lines beginning with '#' */            
   while((c=getc(ficpar))=='#' && c!= EOF){            for(i=1; i<=npar; i++)
     ungetc(c,ficpar);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     fgets(line, MAXLINE, ficpar);      
     puts(line);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     fputs(line,ficparo);            k=0;
   }            for(i=1; i<=(nlstate); i++){
   ungetc(c,ficpar);              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                gm[k]=pmmij[i][j];
   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);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       printf("%1d%1d",i,j);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
       fprintf(ficparo,"%1d%1d",i1,j1);          }
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar,"%le",&delti3[i][j][k]);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
         printf(" %le",delti3[i][j][k]);            for(theta=1; theta <=npar; theta++)
         fprintf(ficparo," %le",delti3[i][j][k]);              trgradg[j][theta]=gradg[theta][j];
       }          
       fscanf(ficpar,"\n");          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
       printf("\n");          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       fprintf(ficparo,"\n");          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     }          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   }          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   delti=delti3[1][1];          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
    
   /* Reads comments: lines beginning with '#' */          pmij(pmmij,cov,ncovmodel,x,nlstate);
   while((c=getc(ficpar))=='#' && c!= EOF){          
     ungetc(c,ficpar);          k=0;
     fgets(line, MAXLINE, ficpar);          for(i=1; i<=(nlstate); i++){
     puts(line);            for(j=1; j<=(nlstate+ndeath);j++){
     fputs(line,ficparo);              k=k+1;
   }              mu[k][(int) age]=pmmij[i][j];
   ungetc(c,ficpar);            }
            }
   matcov=matrix(1,npar,1,npar);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   for(i=1; i <=npar; i++){            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
     fscanf(ficpar,"%s",&str);              varpij[i][j][(int)age] = doldm[i][j];
     printf("%s",str);  
     fprintf(ficparo,"%s",str);          /*printf("\n%d ",(int)age);
     for(j=1; j <=i; j++){            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       fscanf(ficpar," %le",&matcov[i][j]);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       printf(" %.5le",matcov[i][j]);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
       fprintf(ficparo," %.5le",matcov[i][j]);            }*/
     }  
     fscanf(ficpar,"\n");          fprintf(ficresprob,"\n%d ",(int)age);
     printf("\n");          fprintf(ficresprobcov,"\n%d ",(int)age);
     fprintf(ficparo,"\n");          fprintf(ficresprobcor,"\n%d ",(int)age);
   }  
   for(i=1; i <=npar; i++)          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     for(j=i+1;j<=npar;j++)            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       matcov[i][j]=matcov[j][i];          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   printf("\n");            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
     /*-------- Rewriting paramater file ----------*/          for (k=1; k<=(nlstate);k++){
      strcpy(rfileres,"r");    /* "Rparameterfile */            for (l=1; l<=(nlstate+ndeath);l++){ 
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/              i=i++;
      strcat(rfileres,".");    /* */              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     if((ficres =fopen(rfileres,"w"))==NULL) {              for (j=1; j<=i;j++){
       printf("Problem writing new parameter file: %s\n", fileres);goto end;                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     }                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     fprintf(ficres,"#%s\n",version);              }
                }
     /*-------- data file ----------*/          }/* end of loop for state */
     if((fic=fopen(datafile,"r"))==NULL)    {        } /* end of loop for age */
       printf("Problem with datafile: %s\n", datafile);goto end;  
     }        /* Confidence intervalle of pij  */
         /*
     n= lastobs;          fprintf(ficgp,"\nset noparametric;unset label");
     severity = vector(1,maxwav);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     outcome=imatrix(1,maxwav+1,1,n);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     num=ivector(1,n);          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);
     moisnais=vector(1,n);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     annais=vector(1,n);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     moisdc=vector(1,n);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     andc=vector(1,n);        */
     agedc=vector(1,n);  
     cod=ivector(1,n);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     weight=vector(1,n);        first1=1;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        for (k2=1; k2<=(nlstate);k2++){
     mint=matrix(1,maxwav,1,n);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     anint=matrix(1,maxwav,1,n);            if(l2==k2) continue;
     s=imatrix(1,maxwav+1,1,n);            j=(k2-1)*(nlstate+ndeath)+l2;
     adl=imatrix(1,maxwav+1,1,n);                for (k1=1; k1<=(nlstate);k1++){
     tab=ivector(1,NCOVMAX);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     ncodemax=ivector(1,8);                if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
     i=1;                if(i<=j) continue;
     while (fgets(line, MAXLINE, fic) != NULL)    {                for (age=bage; age<=fage; age ++){ 
       if ((i >= firstobs) && (i <=lastobs)) {                  if ((int)age %5==0){
                            v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
         for (j=maxwav;j>=1;j--){                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
           strcpy(line,stra);                    mu1=mu[i][(int) age]/stepm*YEARM ;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                    mu2=mu[j][(int) age]/stepm*YEARM;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                    c12=cv12/sqrt(v1*v2);
         }                    /* Computing eigen value of matrix of covariance */
                            lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);                    /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);                    /*v21=sqrt(1.-v11*v11); *//* error */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);                    v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);                    v22=v11;
         for (j=ncovcol;j>=1;j--){                    tnalp=v21/v11;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                    if(first1==1){
         }                      first1=0;
         num[i]=atol(stra);                      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);
                            }
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
           printf("%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;}*/                    /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
         i=i+1;                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
       }                    if(first==1){
     }                      first=0;
     /* printf("ii=%d", ij);                      fprintf(ficgp,"\nset parametric;unset label");
        scanf("%d",i);*/                      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);
   imx=i-1; /* Number of individuals */                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   /* for (i=1; i<=imx; i++){   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     }*/                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
    /*  for (i=1; i<=imx; i++){                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
      if (s[4][i]==9)  s[4][i]=-1;                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
      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]));}*/                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                        fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                        fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   /* Calculation of the number of parameter from char model*/                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   Tvar=ivector(1,15);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   Tprod=ivector(1,15);                    }else{
   Tvaraff=ivector(1,15);                      first=0;
   Tvard=imatrix(1,15,1,2);                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
   Tage=ivector(1,15);                            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);
   if (strlen(model) >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",\
     j=0, j1=0, k1=1, k2=1;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     j=nbocc(model,'+');                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     j1=nbocc(model,'*');                    }/* if first */
     cptcovn=j+1;                  } /* age mod 5 */
     cptcovprod=j1;                } /* end loop age */
                    fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     strcpy(modelsav,model);                first=1;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){              } /*l12 */
       printf("Error. Non available option model=%s ",model);            } /* k12 */
       goto end;          } /*l1 */
     }        }/* k1 */
          } /* loop covariates */
     for(i=(j+1); i>=1;i--){    }
       cutv(stra,strb,modelsav,'+');    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    free_vector(xp,1,npar);
       /*scanf("%d",i);*/    fclose(ficresprob);
       if (strchr(strb,'*')) {    fclose(ficresprobcov);
         cutv(strd,strc,strb,'*');    fclose(ficresprobcor);
         if (strcmp(strc,"age")==0) {    fflush(ficgp);
           cptcovprod--;    fflush(fichtmcov);
           cutv(strb,stre,strd,'V');  }
           Tvar[i]=atoi(stre);  
           cptcovage++;  
             Tage[cptcovage]=i;  /******************* Printing html file ***********/
             /*printf("stre=%s ", stre);*/  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
         }                    int lastpass, int stepm, int weightopt, char model[],\
         else if (strcmp(strd,"age")==0) {                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
           cptcovprod--;                    int popforecast, int estepm ,\
           cutv(strb,stre,strc,'V');                    double jprev1, double mprev1,double anprev1, \
           Tvar[i]=atoi(stre);                    double jprev2, double mprev2,double anprev2){
           cptcovage++;    int jj1, k1, i1, cpt;
           Tage[cptcovage]=i;    /*char optionfilehtm[FILENAMELENGTH];*/
         }  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
         else {  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
           cutv(strb,stre,strc,'V');  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
           Tvar[i]=ncovcol+k1;  /*   } */
           cutv(strb,strc,strd,'V');  
           Tprod[k1]=i;     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
           Tvard[k1][1]=atoi(strc);   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
           Tvard[k1][2]=atoi(stre);   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
           Tvar[cptcovn+k2]=Tvard[k1][1];   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
           Tvar[cptcovn+k2+1]=Tvard[k1][2];   - Life expectancies by age and initial health status (estepm=%2d months): \
           for (k=1; k<=lastobs;k++)     <a href=\"%s\">%s</a> <br>\n</li>", \
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
           k1++;             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
           k2=k2+2;             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
         }             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
       }  
       else {  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  
        /*  scanf("%d",i);*/   m=cptcoveff;
       cutv(strd,strc,strb,'V');   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       Tvar[i]=atoi(strc);  
       }   jj1=0;
       strcpy(modelsav,stra);     for(k1=1; k1<=m;k1++){
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);     for(i1=1; i1<=ncodemax[k1];i1++){
         scanf("%d",i);*/       jj1++;
     }       if (cptcovn > 0) {
 }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           for (cpt=1; cpt<=cptcoveff;cpt++) 
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   printf("cptcovprod=%d ", cptcovprod);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   scanf("%d ",i);*/       }
     fclose(fic);       /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
     /*  if(mle==1){*/  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
     if (weightopt != 1) { /* Maximisation without weights*/       /* Quasi-incidences */
       for(i=1;i<=n;i++) weight[i]=1.0;       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
     }   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
     /*-calculation of age at interview from date of interview and age at death -*/  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
     agev=matrix(1,maxwav,1,imx);         /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
     for (i=1; i<=imx; i++) {           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
       for(m=2; (m<= maxwav); m++) {  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){         }
          anint[m][i]=9999;       for(cpt=1; cpt<=nlstate;cpt++) {
          s[m][i]=-1;          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
        }  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;       }
       }       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
     }  health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
     for (i=1; i<=imx; i++)  {     } /* end i1 */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);   }/* End k1 */
       for(m=1; (m<= maxwav); m++){   fprintf(fichtm,"</ul>");
         if(s[m][i] >0){  
           if (s[m][i] >= nlstate+1) {  
             if(agedc[i]>0)   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
               if(moisdc[i]!=99 && andc[i]!=9999)   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
                 agev[m][i]=agedc[i];   - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
            else {   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
               if (andc[i]!=9999){   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
               printf("Warning negative age at death: %d line:%d\n",num[i],i);   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
               agev[m][i]=-1;   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
               }           rfileres,rfileres,\
             }           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
           }           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
           else if(s[m][i] !=9){ /* Should no more exist */           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
             if(mint[m][i]==99 || anint[m][i]==9999)           subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
               agev[m][i]=1;           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
             else if(agev[m][i] <agemin){  
               agemin=agev[m][i];  /*  if(popforecast==1) fprintf(fichtm,"\n */
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
             }  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
             else if(agev[m][i] >agemax){  /*      <br>",fileres,fileres,fileres,fileres); */
               agemax=agev[m][i];  /*  else  */
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  /*    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); */
             }  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
             /*agev[m][i]=anint[m][i]-annais[i];*/  
             /*   agev[m][i] = age[i]+2*m;*/   m=cptcoveff;
           }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
           else { /* =9 */  
             agev[m][i]=1;   jj1=0;
             s[m][i]=-1;   for(k1=1; k1<=m;k1++){
           }     for(i1=1; i1<=ncodemax[k1];i1++){
         }       jj1++;
         else /*= 0 Unknown */       if (cptcovn > 0) {
           agev[m][i]=1;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       }         for (cpt=1; cpt<=cptcoveff;cpt++) 
               fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     for (i=1; i<=imx; i++)  {       }
       for(m=1; (m<= maxwav); m++){       for(cpt=1; cpt<=nlstate;cpt++) {
         if (s[m][i] > (nlstate+ndeath)) {         fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
           printf("Error: Wrong value in nlstate or ndeath\n");    interval) in state (%d): %s%d%d.png <br>\
           goto end;  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
         }       }
       }     } /* end i1 */
     }   }/* End k1 */
    fprintf(fichtm,"</ul>");
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);   fflush(fichtm);
   }
     free_vector(severity,1,maxwav);  
     free_imatrix(outcome,1,maxwav+1,1,n);  /******************* Gnuplot file **************/
     free_vector(moisnais,1,n);  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     free_vector(annais,1,n);  
     /* free_matrix(mint,1,maxwav,1,n);    char dirfileres[132],optfileres[132];
        free_matrix(anint,1,maxwav,1,n);*/    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     free_vector(moisdc,1,n);    int ng;
     free_vector(andc,1,n);  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
      /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
     wav=ivector(1,imx);  /*   } */
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    /*#ifdef windows */
        fprintf(ficgp,"cd \"%s\" \n",pathc);
     /* Concatenates waves */      /*#endif */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
       Tcode=ivector(1,100);    strcpy(optfileres,"vpl");
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);   /* 1eme*/
       ncodemax[1]=1;    for (cpt=1; cpt<= nlstate ; cpt ++) {
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);     for (k1=1; k1<= m ; k1 ++) {
             fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
    codtab=imatrix(1,100,1,10);       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
    h=0;       fprintf(ficgp,"set xlabel \"Age\" \n\
    m=pow(2,cptcoveff);  set ylabel \"Probability\" \n\
    set ter png small\n\
    for(k=1;k<=cptcoveff; k++){  set size 0.65,0.65\n\
      for(i=1; i <=(m/pow(2,k));i++){  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
        for(j=1; j <= ncodemax[k]; j++){  
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){       for (i=1; i<= nlstate ; i ++) {
            h++;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;         else fprintf(ficgp," \%%*lf (\%%*lf)");
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/       }
          }       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)");
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);       } 
       codtab[1][2]=1;codtab[2][2]=2; */       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
    /* for(i=1; i <=m ;i++){       for (i=1; i<= nlstate ; i ++) {
       for(k=1; k <=cptcovn; k++){         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       }       }  
       printf("\n");       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
       }     }
       scanf("%d",i);*/    }
        /*2 eme*/
    /* Calculates basic frequencies. Computes observed prevalence at single age    
        and prints on file fileres'p'. */    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);
          
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for (i=1; i<= nlstate+1 ; i ++) {
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        k=2*i;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for (j=1; j<= nlstate+1 ; j ++) {
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
                else fprintf(ficgp," \%%*lf (\%%*lf)");
     /* 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] */        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        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);
     if(mle==1){        for (j=1; j<= nlstate+1 ; j ++) {
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     }          else fprintf(ficgp," \%%*lf (\%%*lf)");
            }   
     /*--------- results files --------------*/        fprintf(ficgp,"\" t\"\" w l 0,");
     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(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
          for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
    jk=1;          else fprintf(ficgp," \%%*lf (\%%*lf)");
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        }   
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
    for(i=1,jk=1; i <=nlstate; i++){        else fprintf(ficgp,"\" t\"\" w l 0,");
      for(k=1; k <=(nlstate+ndeath); k++){      }
        if (k != i)    }
          {    
            printf("%d%d ",i,k);    /*3eme*/
            fprintf(ficres,"%1d%1d ",i,k);    
            for(j=1; j <=ncovmodel; j++){    for (k1=1; k1<= m ; k1 ++) { 
              printf("%f ",p[jk]);      for (cpt=1; cpt<= nlstate ; cpt ++) {
              fprintf(ficres,"%f ",p[jk]);        k=2+nlstate*(2*cpt-2);
              jk++;        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
            }        fprintf(ficgp,"set ter png small\n\
            printf("\n");  set size 0.65,0.65\n\
            fprintf(ficres,"\n");  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
          }        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
      }          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
    }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
  if(mle==1){          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     /* Computing hessian and covariance matrix */          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     ftolhess=ftol; /* Usually correct */          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     hesscov(matcov, p, npar, delti, ftolhess, func);          
  }        */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");        for (i=1; i< nlstate ; i ++) {
     printf("# Scales (for hessian or gradient estimation)\n");          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);
      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);    
           for(k=1; k<=ncovmodel;k++){    /* CV preval stable (period) */
             printf(" %.5e",delti[jk]);    for (k1=1; k1<= m ; k1 ++) { 
             fprintf(ficres," %.5e",delti[jk]);      for (cpt=1; cpt<=nlstate ; cpt ++) {
             jk++;        k=3;
           }        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
           printf("\n");        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
           fprintf(ficres,"\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/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
      }        
            for (i=1; i< nlstate ; i ++)
     k=1;          fprintf(ficgp,"+$%d",k+i+1);
     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");        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+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");        
     for(i=1;i<=npar;i++){        l=3+(nlstate+ndeath)*cpt;
       /*  if (k>nlstate) k=1;        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
       i1=(i-1)/(ncovmodel*nlstate)+1;        for (i=1; i< nlstate ; i ++) {
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          l=3+(nlstate+ndeath)*cpt;
       printf("%s%d%d",alph[k],i1,tab[i]);*/          fprintf(ficgp,"+$%d",l+i+1);
       fprintf(ficres,"%3d",i);        }
       printf("%3d",i);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       for(j=1; j<=i;j++){      } 
         fprintf(ficres," %.5e",matcov[i][j]);    }  
         printf(" %.5e",matcov[i][j]);    
       }    /* proba elementaires */
       fprintf(ficres,"\n");    for(i=1,jk=1; i <=nlstate; i++){
       printf("\n");      for(k=1; k <=(nlstate+ndeath); k++){
       k++;        if (k != i) {
     }          for(j=1; j <=ncovmodel; j++){
                fprintf(ficgp,"p%d=%f ",jk,p[jk]);
     while((c=getc(ficpar))=='#' && c!= EOF){            jk++; 
       ungetc(c,ficpar);            fprintf(ficgp,"\n");
       fgets(line, MAXLINE, ficpar);          }
       puts(line);        }
       fputs(line,ficparo);      }
     }     }
     ungetc(c,ficpar);  
     estepm=0;     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);       for(jk=1; jk <=m; jk++) {
     if (estepm==0 || estepm < stepm) estepm=stepm;         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
     if (fage <= 2) {         if (ng==2)
       bage = ageminpar;           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
       fage = agemaxpar;         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);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");         i=1;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);         for(k2=1; k2<=nlstate; k2++) {
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);           k3=i;
             for(k=1; k<=(nlstate+ndeath); k++) {
     while((c=getc(ficpar))=='#' && c!= EOF){             if (k != k2){
     ungetc(c,ficpar);               if(ng==2)
     fgets(line, MAXLINE, ficpar);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
     puts(line);               else
     fputs(line,ficparo);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   }               ij=1;
   ungetc(c,ficpar);               for(j=3; j <=ncovmodel; j++) {
                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                   ij++;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                 }
                       else
   while((c=getc(ficpar))=='#' && c!= EOF){                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     ungetc(c,ficpar);               }
     fgets(line, MAXLINE, ficpar);               fprintf(ficgp,")/(1");
     puts(line);               
     fputs(line,ficparo);               for(k1=1; k1 <=nlstate; k1++){   
   }                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   ungetc(c,ficpar);                 ij=1;
                   for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                     ij++;
                    }
   fscanf(ficpar,"pop_based=%d\n",&popbased);                   else
   fprintf(ficparo,"pop_based=%d\n",popbased);                       fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   fprintf(ficres,"pop_based=%d\n",popbased);                   }
                   fprintf(ficgp,")");
   while((c=getc(ficpar))=='#' && c!= EOF){               }
     ungetc(c,ficpar);               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
     fgets(line, MAXLINE, ficpar);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     puts(line);               i=i+ncovmodel;
     fputs(line,ficparo);             }
   }           } /* end k */
   ungetc(c,ficpar);         } /* end k2 */
        } /* end jk */
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);     } /* end ng */
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);     fflush(ficgp); 
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  }  /* end gnuplot */
   
   
 while((c=getc(ficpar))=='#' && c!= EOF){  /*************** Moving average **************/
     ungetc(c,ficpar);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
     fgets(line, MAXLINE, ficpar);  
     puts(line);    int i, cpt, cptcod;
     fputs(line,ficparo);    int modcovmax =1;
   }    int mobilavrange, mob;
   ungetc(c,ficpar);    double age;
   
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                             a covariate has 2 modalities */
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
 /*------------ gnuplot -------------*/      else mobilavrange=mobilav;
   strcpy(optionfilegnuplot,optionfilefiname);      for (age=bage; age<=fage; age++)
   strcat(optionfilegnuplot,".gp");        for (i=1; i<=nlstate;i++)
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {          for (cptcod=1;cptcod<=modcovmax;cptcod++)
     printf("Problem with file %s",optionfilegnuplot);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   }      /* We keep the original values on the extreme ages bage, fage and for 
   fclose(ficgp);         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);         we use a 5 terms etc. until the borders are no more concerned. 
 /*--------- index.htm --------*/      */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
   strcpy(optionfilehtm,optionfile);        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
   strcat(optionfilehtm,".htm");          for (i=1; i<=nlstate;i++){
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {            for (cptcod=1;cptcod<=modcovmax;cptcod++){
     printf("Problem with %s \n",optionfilehtm), exit(0);              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];
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n                }
 \n              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
 Total number of observations=%d <br>\n            }
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n          }
 <hr  size=\"2\" color=\"#EC5E5E\">        }/* end age */
  <ul><li><h4>Parameter files</h4>\n      }/* end mob */
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    }else return -1;
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);    return 0;
   fclose(fichtm);  }/* End movingaverage */
   
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);  
    /************** Forecasting ******************/
 /*------------ free_vector  -------------*/  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){
  chdir(path);    /* proj1, year, month, day of starting projection 
         agemin, agemax range of age
  free_ivector(wav,1,imx);       dateprev1 dateprev2 range of dates during which prevalence is computed
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);       anproj2 year of en of projection (same day and month as proj1).
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      */
  free_ivector(num,1,n);    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
  free_vector(agedc,1,n);    int *popage;
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    double agec; /* generic age */
  fclose(ficparo);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
  fclose(ficres);    double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
   /*--------------- Prevalence limit --------------*/    char fileresf[FILENAMELENGTH];
    
   strcpy(filerespl,"pl");    agelim=AGESUP;
   strcat(filerespl,fileres);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {   
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    strcpy(fileresf,"f"); 
   }    strcat(fileresf,fileres);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    if((ficresf=fopen(fileresf,"w"))==NULL) {
   fprintf(ficrespl,"#Prevalence limit\n");      printf("Problem with forecast resultfile: %s\n", fileresf);
   fprintf(ficrespl,"#Age ");      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    }
   fprintf(ficrespl,"\n");    printf("Computing forecasting: result on file '%s' \n", fileresf);
      fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if (mobilav!=0) {
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   k=0;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   agebase=ageminpar;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   agelim=agemaxpar;      }
   ftolpl=1.e-10;    }
   i1=cptcoveff;  
   if (cptcovn < 1){i1=1;}    stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
   for(cptcov=1;cptcov<=i1;cptcov++){    if(estepm < stepm){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      printf ("Problem %d lower than %d\n",estepm, stepm);
         k=k+1;    }
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    else  hstepm=estepm;   
         fprintf(ficrespl,"\n#******");  
         for(j=1;j<=cptcoveff;j++)    hstepm=hstepm/stepm; 
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
         fprintf(ficrespl,"******\n");                                 fractional in yp1 */
            anprojmean=yp;
         for (age=agebase; age<=agelim; age++){    yp2=modf((yp1*12),&yp);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    mprojmean=yp;
           fprintf(ficrespl,"%.0f",age );    yp1=modf((yp2*30.5),&yp);
           for(i=1; i<=nlstate;i++)    jprojmean=yp;
           fprintf(ficrespl," %.5f", prlim[i][i]);    if(jprojmean==0) jprojmean=1;
           fprintf(ficrespl,"\n");    if(mprojmean==0) jprojmean=1;
         }  
       }    i1=cptcoveff;
     }    if (cptcovn < 1){i1=1;}
   fclose(ficrespl);    
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
   /*------------- h Pij x at various ages ------------*/    
      fprintf(ficresf,"#****** Routine prevforecast **\n");
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  /*            if (h==(int)(YEARM*yearp)){ */
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
   }      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   printf("Computing pij: result on file '%s' \n", filerespij);        k=k+1;
          fprintf(ficresf,"\n#******");
   stepsize=(int) (stepm+YEARM-1)/YEARM;        for(j=1;j<=cptcoveff;j++) {
   /*if (stepm<=24) stepsize=2;*/          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]]);
         }
   agelim=AGESUP;        fprintf(ficresf,"******\n");
   hstepm=stepsize*YEARM; /* Every year of age */        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */        for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
   /* hstepm=1;   aff par mois*/            fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
   k=0;        }
   for(cptcov=1;cptcov<=i1;cptcov++){        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficresf,"\n");
       k=k+1;          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)          for (agec=fage; agec>=(ageminpar-1); agec--){ 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
         fprintf(ficrespij,"******\n");            nhstepm = nhstepm/hstepm; 
                    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */            oldm=oldms;savm=savms;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          
             for (h=0; h<=nhstepm; h++){
           /*      nhstepm=nhstepm*YEARM; aff par mois*/              if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                for(j=1;j<=cptcoveff;j++) 
           oldm=oldms;savm=savms;                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                  fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
           fprintf(ficrespij,"# Age");              } 
           for(i=1; i<=nlstate;i++)              for(j=1; j<=nlstate+ndeath;j++) {
             for(j=1; j<=nlstate+ndeath;j++)                ppij=0.;
               fprintf(ficrespij," %1d-%1d",i,j);                for(i=1; i<=nlstate;i++) {
           fprintf(ficrespij,"\n");                  if (mobilav==1) 
            for (h=0; h<=nhstepm; h++){                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                  else {
             for(i=1; i<=nlstate;i++)                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
               for(j=1; j<=nlstate+ndeath;j++)                  }
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                  if (h*hstepm/YEARM*stepm== yearp) {
             fprintf(ficrespij,"\n");                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
              }                  }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                } /* end i */
           fprintf(ficrespij,"\n");                if (h*hstepm/YEARM*stepm==yearp) {
         }                  fprintf(ficresf," %.3f", ppij);
     }                }
   }              }/* end j */
             } /* end h */
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
   fclose(ficrespij);        } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
   /*---------- Forecasting ------------------*/         
   if((stepm == 1) && (strcmp(model,".")==0)){    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);  
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    fclose(ficresf);
   }  }
   else{  
     erreur=108;  /************** Forecasting *****not tested NB*************/
     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);  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;
   /*---------- Health expectancies and variances ------------*/    double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
   strcpy(filerest,"t");    double ***p3mat,***tabpop,***tabpopprev;
   strcat(filerest,fileres);    double ***mobaverage;
   if((ficrest=fopen(filerest,"w"))==NULL) {    char filerespop[FILENAMELENGTH];
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
   }    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
   strcpy(filerese,"e");    
   strcat(filerese,fileres);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    
   }    strcpy(filerespop,"pop"); 
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
  strcpy(fileresv,"v");      printf("Problem with forecast resultfile: %s\n", filerespop);
   strcat(fileresv,fileres);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    }
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    printf("Computing forecasting: result on file '%s' \n", filerespop);
   }    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  
   calagedate=-1;    if (cptcoveff==0) ncodemax[cptcoveff]=1;
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
     if (mobilav!=0) {
   k=0;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   for(cptcov=1;cptcov<=i1;cptcov++){      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       k=k+1;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       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");    stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
       fprintf(ficreseij,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)    agelim=AGESUP;
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       fprintf(ficreseij,"******\n");    hstepm=1;
     hstepm=hstepm/stepm; 
       fprintf(ficresvij,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)    if (popforecast==1) {
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      if((ficpop=fopen(popfile,"r"))==NULL) {
       fprintf(ficresvij,"******\n");        printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      } 
       oldm=oldms;savm=savms;      popage=ivector(0,AGESUP);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);        popeffectif=vector(0,AGESUP);
        popcount=vector(0,AGESUP);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      
       oldm=oldms;savm=savms;      i=1;   
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);      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];
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  
       fprintf(ficrest,"\n");    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
       epj=vector(1,nlstate+1);        k=k+1;
       for(age=bage; age <=fage ;age++){        fprintf(ficrespop,"\n#******");
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        for(j=1;j<=cptcoveff;j++) {
         if (popbased==1) {          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)        }
             prlim[i][i]=probs[(int)age][i][k];        fprintf(ficrespop,"******\n");
         }        fprintf(ficrespop,"# Age");
                for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         fprintf(ficrest," %4.0f",age);        if (popforecast==1)  fprintf(ficrespop," [Population]");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){        
           for(i=1, epj[j]=0.;i <=nlstate;i++) {        for (cpt=0; cpt<=0;cpt++) { 
             epj[j] += prlim[i][i]*eij[i][j][(int)age];          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/          
           }          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
           epj[nlstate+1] +=epj[j];            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
         }            nhstepm = nhstepm/hstepm; 
             
         for(i=1, vepp=0.;i <=nlstate;i++)            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           for(j=1;j <=nlstate;j++)            oldm=oldms;savm=savms;
             vepp += vareij[i][j][(int)age];            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));          
         for(j=1;j <=nlstate;j++){            for (h=0; h<=nhstepm; h++){
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));              if (h==(int) (calagedatem+YEARM*cpt)) {
         }                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
         fprintf(ficrest,"\n");              } 
       }              for(j=1; j<=nlstate+ndeath;j++) {
     }                kk1=0.;kk2=0;
   }                for(i=1; i<=nlstate;i++) {              
 free_matrix(mint,1,maxwav,1,n);                  if (mobilav==1) 
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
     free_vector(weight,1,n);                  else {
   fclose(ficreseij);                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
   fclose(ficresvij);                  }
   fclose(ficrest);                }
   fclose(ficpar);                if (h==(int)(calagedatem+12*cpt)){
   free_vector(epj,1,nlstate+1);                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
                      /*fprintf(ficrespop," %.3f", kk1);
   /*------- Variance limit prevalence------*/                        if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
   strcpy(fileresvpl,"vpl");              }
   strcat(fileresvpl,fileres);              for(i=1; i<=nlstate;i++){
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {                kk1=0.;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);                  for(j=1; j<=nlstate;j++){
     exit(0);                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
   }                  }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
       k=k+1;            }
       fprintf(ficresvpl,"\n#****** ");            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       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;        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          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; 
   fclose(ficresvpl);            
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*---------- End : free ----------------*/            oldm=oldms;savm=savms;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
              for (h=0; h<=nhstepm; h++){
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);              if (h==(int) (calagedatem+YEARM*cpt)) {
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
                } 
                for(j=1; j<=nlstate+ndeath;j++) {
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);                kk1=0.;kk2=0;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);                for(i=1; i<=nlstate;i++) {              
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                }
                  if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
   free_matrix(matcov,1,npar,1,npar);              }
   free_vector(delti,1,npar);            }
   free_matrix(agev,1,maxwav,1,imx);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);          }
         }
   fprintf(fichtm,"\n</body>");     } 
   fclose(fichtm);    }
   fclose(ficgp);   
      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
   if(erreur >0)    if (popforecast==1) {
     printf("End of Imach with error or warning %d\n",erreur);      free_ivector(popage,0,AGESUP);
   else   printf("End of Imach\n");      free_vector(popeffectif,0,AGESUP);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      free_vector(popcount,0,AGESUP);
      }
   /* 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);*/    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   /*printf("Total time was %d uSec.\n", total_usecs);*/    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   /*------ End -----------*/    fclose(ficrespop);
   } /* End of popforecast */
   
  end:  int fileappend(FILE *fichier, char *optionfich)
 #ifdef windows  {
   /* chdir(pathcd);*/    if((fichier=fopen(optionfich,"a"))==NULL) {
 #endif      printf("Problem with file: %s\n", optionfich);
  /*system("wgnuplot graph.plt");*/      fprintf(ficlog,"Problem with file: %s\n", optionfich);
  /*system("../gp37mgw/wgnuplot graph.plt");*/      return (0);
  /*system("cd ../gp37mgw");*/    }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    fflush(fichier);
  strcpy(plotcmd,GNUPLOTPROGRAM);    return (1);
  strcat(plotcmd," ");  }
  strcat(plotcmd,optionfilegnuplot);  
  system(plotcmd);  
   /**************** function prwizard **********************/
 #ifdef windows  void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   while (z[0] != 'q') {  {
     /* chdir(path); */  
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    /* Wizard to print covariance matrix template */
     scanf("%s",z);  
     if (z[0] == 'c') system("./imach");    char ca[32], cb[32], cc[32];
     else if (z[0] == 'e') system(optionfilehtm);    int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     else if (z[0] == 'g') system(plotcmd);    int numlinepar;
     else if (z[0] == 'q') exit(0);  
   }    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
 #endif    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 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, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     /*  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;
    
     /*   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);
     
   
     jk=1;
     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");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     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 warnings %d\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.1.49  
changed lines
  Added in v.1.94


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