Diff for /imach/src/imach.c between versions 1.47 and 1.101

version 1.47, 2002/06/10 13:12:01 version 1.101, 2004/09/15 10:38:38
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.101  2004/09/15 10:38:38  brouard
      Fix on curr_time
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.100  2004/07/12 18:29:06  brouard
   first survey ("cross") where individuals from different ages are    Add version for Mac OS X. Just define UNIX in Makefile
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.99  2004/06/05 08:57:40  brouard
   second wave of interviews ("longitudinal") which measure each change    *** empty log message ***
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.98  2004/05/16 15:05:56  brouard
   model. More health states you consider, more time is necessary to reach the    New version 0.97 . First attempt to estimate force of mortality
   Maximum Likelihood of the parameters involved in the model.  The    directly from the data i.e. without the need of knowing the health
   simplest model is the multinomial logistic model where pij is the    state at each age, but using a Gompertz model: log u =a + b*age .
   probability to be observed in state j at the second wave    This is the basic analysis of mortality and should be done before any
   conditional to be observed in state i at the first wave. Therefore    other analysis, in order to test if the mortality estimated from the
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    cross-longitudinal survey is different from the mortality estimated
   'age' is age and 'sex' is a covariate. If you want to have a more    from other sources like vital statistic data.
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    The same imach parameter file can be used but the option for mle should be -3.
   you to do it.  More covariates you add, slower the  
   convergence.    Agnès, who wrote this part of the code, tried to keep most of the
     former routines in order to include the new code within the former code.
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    The output is very simple: only an estimate of the intercept and of
   identical for each individual. Also, if a individual missed an    the slope with 95% confident intervals.
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Current limitations:
     A) Even if you enter covariates, i.e. with the
   hPijx is the probability to be observed in state i at age x+h    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   conditional to the observed state i at age x. The delay 'h' can be    B) There is no computation of Life Expectancy nor Life Table.
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    Revision 1.97  2004/02/20 13:25:42  lievre
   semester or year) is model as a multinomial logistic.  The hPx    Version 0.96d. Population forecasting command line is (temporarily)
   matrix is simply the matrix product of nh*stepm elementary matrices    suppressed.
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   Also this programme outputs the covariance matrix of the parameters but also    rewritten within the same printf. Workaround: many printfs.
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.95  2003/07/08 07:54:34  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    * imach.c (Repository):
            Institut national d'études démographiques, Paris.    (Repository): Using imachwizard code to output a more meaningful covariance
   This software have been partly granted by Euro-REVES, a concerted action    matrix (cov(a12,c31) instead of numbers.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.94  2003/06/27 13:00:02  brouard
   software can be distributed freely for non commercial use. Latest version    Just cleaning
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.93  2003/06/25 16:33:55  brouard
      (Module): On windows (cygwin) function asctime_r doesn't
 #include <math.h>    exist so I changed back to asctime which exists.
 #include <stdio.h>    (Module): Version 0.96b
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 #define MAXLINE 256    exist so I changed back to asctime which exists.
 #define GNUPLOTPROGRAM "gnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.91  2003/06/25 15:30:29  brouard
 #define FILENAMELENGTH 80    * imach.c (Repository): Duplicated warning errors corrected.
 /*#define DEBUG*/    (Repository): Elapsed time after each iteration is now output. It
 #define windows    helps to forecast when convergence will be reached. Elapsed time
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    is stamped in powell.  We created a new html file for the graphs
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    concerning matrix of covariance. It has extension -cov.htm.
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.90  2003/06/24 12:34:15  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 #define NINTERVMAX 8    of the covariance matrix to be input.
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.89  2003/06/24 12:30:52  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    (Module): Some bugs corrected for windows. Also, when
 #define MAXN 20000    mle=-1 a template is output in file "or"mypar.txt with the design
 #define YEARM 12. /* Number of months per year */    of the covariance matrix to be input.
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.88  2003/06/23 17:54:56  brouard
 #ifdef windows    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
 #define DIRSEPARATOR '\\'  
 #else    Revision 1.87  2003/06/18 12:26:01  brouard
 #define DIRSEPARATOR '/'    Version 0.96
 #endif  
     Revision 1.86  2003/06/17 20:04:08  brouard
 char version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";    (Module): Change position of html and gnuplot routines and added
 int erreur; /* Error number */    routine fileappend.
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.85  2003/06/17 13:12:43  brouard
 int npar=NPARMAX;    * imach.c (Repository): Check when date of death was earlier that
 int nlstate=2; /* Number of live states */    current date of interview. It may happen when the death was just
 int ndeath=1; /* Number of dead states */    prior to the death. In this case, dh was negative and likelihood
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    was wrong (infinity). We still send an "Error" but patch by
 int popbased=0;    assuming that the date of death was just one stepm after the
     interview.
 int *wav; /* Number of waves for this individuual 0 is possible */    (Repository): Because some people have very long ID (first column)
 int maxwav; /* Maxim number of waves */    we changed int to long in num[] and we added a new lvector for
 int jmin, jmax; /* min, max spacing between 2 waves */    memory allocation. But we also truncated to 8 characters (left
 int mle, weightopt;    truncation)
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Repository): No more line truncation errors.
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.84  2003/06/13 21:44:43  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    * imach.c (Repository): Replace "freqsummary" at a correct
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    place. It differs from routine "prevalence" which may be called
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    many times. Probs is memory consuming and must be used with
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    parcimony.
 FILE *fichtm; /* Html File */    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 FILE *ficreseij;  
 char filerese[FILENAMELENGTH];    Revision 1.83  2003/06/10 13:39:11  lievre
 FILE  *ficresvij;    *** empty log message ***
 char fileresv[FILENAMELENGTH];  
 FILE  *ficresvpl;    Revision 1.82  2003/06/05 15:57:20  brouard
 char fileresvpl[FILENAMELENGTH];    Add log in  imach.c and  fullversion number is now printed.
 char title[MAXLINE];  
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  */
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  /*
      Interpolated Markov Chain
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  
     Short summary of the programme:
 char filerest[FILENAMELENGTH];    
 char fileregp[FILENAMELENGTH];    This program computes Healthy Life Expectancies from
 char popfile[FILENAMELENGTH];    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    interviewed on their health status or degree of disability (in the
     case of a health survey which is our main interest) -2- at least a
 #define NR_END 1    second wave of interviews ("longitudinal") which measure each change
 #define FREE_ARG char*    (if any) in individual health status.  Health expectancies are
 #define FTOL 1.0e-10    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
 #define NRANSI    Maximum Likelihood of the parameters involved in the model.  The
 #define ITMAX 200    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
 #define TOL 2.0e-4    conditional to be observed in state i at the first wave. Therefore
     the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #define CGOLD 0.3819660    'age' is age and 'sex' is a covariate. If you want to have a more
 #define ZEPS 1.0e-10    complex model than "constant and age", you should modify the program
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
 #define GOLD 1.618034    convergence.
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
 static double maxarg1,maxarg2;    identical for each individual. Also, if a individual missed an
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    intermediate interview, the information is lost, but taken into
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    account using an interpolation or extrapolation.  
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    hPijx is the probability to be observed in state i at age x+h
 #define rint(a) floor(a+0.5)    conditional to the observed state i at age x. The delay 'h' can be
     split into an exact number (nh*stepm) of unobserved intermediate
 static double sqrarg;    states. This elementary transition (by month, quarter,
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    semester or year) is modelled as a multinomial logistic.  The hPx
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
 int imx;    hPijx.
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the stable prevalence. 
 int estepm;    
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
 int m,nb;    This software have been partly granted by Euro-REVES, a concerted action
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    from the European Union.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    It is copyrighted identically to a GNU software product, ie programme and
 double **pmmij, ***probs, ***mobaverage;    software can be distributed freely for non commercial use. Latest version
 double dateintmean=0;    can be accessed at http://euroreves.ined.fr/imach .
   
 double *weight;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 int **s; /* Status */    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 double *agedc, **covar, idx;    
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    **********************************************************************/
   /*
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    main
 double ftolhess; /* Tolerance for computing hessian */    read parameterfile
     read datafile
 /**************** split *************************/    concatwav
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    freqsummary
 {    if (mle >= 1)
    char *s;                             /* pointer */      mlikeli
    int  l1, l2;                         /* length counters */    print results files
     if mle==1 
    l1 = strlen( path );                 /* length of path */       computes hessian
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    read end of parameter file: agemin, agemax, bage, fage, estepm
    s = strrchr( path,  DIRSEPARATOR );          /* find last / */        begin-prev-date,...
    if ( s == NULL ) {                   /* no directory, so use current */    open gnuplot file
 #if     defined(__bsd__)                /* get current working directory */    open html file
       extern char       *getwd( );    stable prevalence
      for age prevalim()
       if ( getwd( dirc ) == NULL ) {    h Pij x
 #else    variance of p varprob
       extern char       *getcwd( );    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Variance-covariance of DFLE
 #endif    prevalence()
          return( GLOCK_ERROR_GETCWD );     movingaverage()
       }    varevsij() 
       strcpy( name, path );             /* we've got it */    if popbased==1 varevsij(,popbased)
    } else {                             /* strip direcotry from path */    total life expectancies
       s++;                              /* after this, the filename */    Variance of stable prevalence
       l2 = strlen( s );                 /* length of filename */   end
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  */
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */  
    }   
    l1 = strlen( dirc );                 /* length of directory */  #include <math.h>
 #ifdef windows  #include <stdio.h>
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #include <stdlib.h>
 #else  #include <unistd.h>
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif  /* #include <sys/time.h> */
    s = strrchr( name, '.' );            /* find last / */  #include <time.h>
    s++;  #include "timeval.h"
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);  /* #include <libintl.h> */
    l2= strlen( s)+1;  /* #define _(String) gettext (String) */
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;  #define MAXLINE 256
    return( 0 );                         /* we're done */  #define GNUPLOTPROGRAM "gnuplot"
 }  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
   /*#define DEBUG*/
 /******************************************/  /*#define windows*/
   #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 void replace(char *s, char*t)  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 {  
   int i;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   int lg=20;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   i=0;  
   lg=strlen(t);  #define NINTERVMAX 8
   for(i=0; i<= lg; i++) {  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
     (s[i] = t[i]);  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
     if (t[i]== '\\') s[i]='/';  #define NCOVMAX 8 /* Maximum number of covariates */
   }  #define MAXN 20000
 }  #define YEARM 12. /* Number of months per year */
   #define AGESUP 130
 int nbocc(char *s, char occ)  #define AGEBASE 40
 {  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   int i,j=0;  #ifdef UNIX
   int lg=20;  #define DIRSEPARATOR '/'
   i=0;  #define ODIRSEPARATOR '\\'
   lg=strlen(s);  #else
   for(i=0; i<= lg; i++) {  #define DIRSEPARATOR '\\'
   if  (s[i] == occ ) j++;  #define ODIRSEPARATOR '/'
   }  #endif
   return j;  
 }  /* $Id$ */
   /* $State$ */
 void cutv(char *u,char *v, char*t, char occ)  
 {  char version[]="Imach version 0.97b, May 2004, INED-EUROREVES ";
   int i,lg,j,p=0;  char fullversion[]="$Revision$ $Date$"; 
   i=0;  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   for(j=0; j<=strlen(t)-1; j++) {  int nvar;
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   }  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
   lg=strlen(t);  int ndeath=1; /* Number of dead states */
   for(j=0; j<p; j++) {  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
     (u[j] = t[j]);  int popbased=0;
   }  
      u[p]='\0';  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav; /* Maxim number of waves */
    for(j=0; j<= lg; j++) {  int jmin, jmax; /* min, max spacing between 2 waves */
     if (j>=(p+1))(v[j-p-1] = t[j]);  int gipmx, gsw; /* Global variables on the number of contributions 
   }                     to the likelihood and the sum of weights (done by funcone)*/
 }  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 /********************** nrerror ********************/  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
 void nrerror(char error_text[])             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 {  double jmean; /* Mean space between 2 waves */
   fprintf(stderr,"ERREUR ...\n");  double **oldm, **newm, **savm; /* Working pointers to matrices */
   fprintf(stderr,"%s\n",error_text);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   exit(1);  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 }  FILE *ficlog, *ficrespow;
 /*********************** vector *******************/  int globpr; /* Global variable for printing or not */
 double *vector(int nl, int nh)  double fretone; /* Only one call to likelihood */
 {  long ipmx; /* Number of contributions */
   double *v;  double sw; /* Sum of weights */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  char filerespow[FILENAMELENGTH];
   if (!v) nrerror("allocation failure in vector");  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   return v-nl+NR_END;  FILE *ficresilk;
 }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
 /************************ free vector ******************/  FILE *fichtm, *fichtmcov; /* Html File */
 void free_vector(double*v, int nl, int nh)  FILE *ficreseij;
 {  char filerese[FILENAMELENGTH];
   free((FREE_ARG)(v+nl-NR_END));  FILE  *ficresvij;
 }  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
 /************************ivector *******************************/  char fileresvpl[FILENAMELENGTH];
 int *ivector(long nl,long nh)  char title[MAXLINE];
 {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   int *v;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   if (!v) nrerror("allocation failure in ivector");  char command[FILENAMELENGTH];
   return v-nl+NR_END;  int  outcmd=0;
 }  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)  char filelog[FILENAMELENGTH]; /* Log file */
 {  char filerest[FILENAMELENGTH];
   free((FREE_ARG)(v+nl-NR_END));  char fileregp[FILENAMELENGTH];
 }  char popfile[FILENAMELENGTH];
   
 /******************* imatrix *******************************/  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 {  struct timezone tzp;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  extern int gettimeofday();
   int **m;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
    long time_value;
   /* allocate pointers to rows */  extern long time();
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  char strcurr[80], strfor[80];
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  #define NR_END 1
   m -= nrl;  #define FREE_ARG char*
    #define FTOL 1.0e-10
    
   /* allocate rows and set pointers to them */  #define NRANSI 
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #define ITMAX 200 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  #define TOL 2.0e-4 
   m[nrl] -= ncl;  
    #define CGOLD 0.3819660 
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  #define ZEPS 1.0e-10 
    #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   /* return pointer to array of pointers to rows */  
   return m;  #define GOLD 1.618034 
 }  #define GLIMIT 100.0 
   #define TINY 1.0e-20 
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)  static double maxarg1,maxarg2;
       int **m;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       long nch,ncl,nrh,nrl;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
      /* free an int matrix allocated by imatrix() */    
 {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #define rint(a) floor(a+0.5)
   free((FREE_ARG) (m+nrl-NR_END));  
 }  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 /******************* matrix *******************************/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 double **matrix(long nrl, long nrh, long ncl, long nch)  int agegomp= AGEGOMP;
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  int imx; 
   double **m;  int stepm=1;
   /* Stepm, step in month: minimum step interpolation*/
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  int estepm;
   m += NR_END;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   m -= nrl;  
   int m,nb;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  long *num;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   m[nrl] += NR_END;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   m[nrl] -= ncl;  double **pmmij, ***probs;
   double *ageexmed,*agecens;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  double dateintmean=0;
   return m;  
 }  double *weight;
   int **s; /* Status */
 /*************************free matrix ************************/  double *agedc, **covar, idx;
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   free((FREE_ARG)(m+nrl-NR_END));  double ftolhess; /* Tolerance for computing hessian */
 }  
   /**************** split *************************/
 /******************* ma3x *******************************/  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  {
 {    /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   double ***m;    */ 
     char  *ss;                            /* pointer */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    int   l1, l2;                         /* length counters */
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    l1 = strlen(path );                   /* length of path */
   m -= nrl;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    if ( ss == NULL ) {                   /* no directory, so use current */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   m[nrl] += NR_END;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   m[nrl] -= ncl;      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         return( GLOCK_ERROR_GETCWD );
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));      }
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");      strcpy( name, path );               /* we've got it */
   m[nrl][ncl] += NR_END;    } else {                              /* strip direcotry from path */
   m[nrl][ncl] -= nll;      ss++;                               /* after this, the filename */
   for (j=ncl+1; j<=nch; j++)      l2 = strlen( ss );                  /* length of filename */
     m[nrl][j]=m[nrl][j-1]+nlay;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
        strcpy( name, ss );         /* save file name */
   for (i=nrl+1; i<=nrh; i++) {      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;      dirc[l1-l2] = 0;                    /* add zero */
     for (j=ncl+1; j<=nch; j++)    }
       m[i][j]=m[i][j-1]+nlay;    l1 = strlen( dirc );                  /* length of directory */
   }    /*#ifdef windows
   return m;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 }  #else
     if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 /*************************free ma3x ************************/  #endif
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    */
 {    ss = strrchr( name, '.' );            /* find last / */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    if (ss >0){
   free((FREE_ARG)(m[nrl]+ncl-NR_END));      ss++;
   free((FREE_ARG)(m+nrl-NR_END));      strcpy(ext,ss);                     /* save extension */
 }      l1= strlen( name);
       l2= strlen(ss)+1;
 /***************** f1dim *************************/      strncpy( finame, name, l1-l2);
 extern int ncom;      finame[l1-l2]= 0;
 extern double *pcom,*xicom;    }
 extern double (*nrfunc)(double []);    return( 0 );                          /* we're done */
    }
 double f1dim(double x)  
 {  
   int j;  /******************************************/
   double f;  
   double *xt;  void replace_back_to_slash(char *s, char*t)
    {
   xt=vector(1,ncom);    int i;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    int lg=0;
   f=(*nrfunc)(xt);    i=0;
   free_vector(xt,1,ncom);    lg=strlen(t);
   return f;    for(i=0; i<= lg; i++) {
 }      (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
 /*****************brent *************************/    }
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  }
 {  
   int iter;  int nbocc(char *s, char occ)
   double a,b,d,etemp;  {
   double fu,fv,fw,fx;    int i,j=0;
   double ftemp;    int lg=20;
   double p,q,r,tol1,tol2,u,v,w,x,xm;    i=0;
   double e=0.0;    lg=strlen(s);
      for(i=0; i<= lg; i++) {
   a=(ax < cx ? ax : cx);    if  (s[i] == occ ) j++;
   b=(ax > cx ? ax : cx);    }
   x=w=v=bx;    return j;
   fw=fv=fx=(*f)(x);  }
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);  void cutv(char *u,char *v, char*t, char occ)
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  {
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    /* cuts string t into u and v where u is ended by char occ excluding it
     printf(".");fflush(stdout);       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 #ifdef DEBUG       gives u="abcedf" and v="ghi2j" */
     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);    int i,lg,j,p=0;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    i=0;
 #endif    for(j=0; j<=strlen(t)-1; j++) {
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       *xmin=x;    }
       return fx;  
     }    lg=strlen(t);
     ftemp=fu;    for(j=0; j<p; j++) {
     if (fabs(e) > tol1) {      (u[j] = t[j]);
       r=(x-w)*(fx-fv);    }
       q=(x-v)*(fx-fw);       u[p]='\0';
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);     for(j=0; j<= lg; j++) {
       if (q > 0.0) p = -p;      if (j>=(p+1))(v[j-p-1] = t[j]);
       q=fabs(q);    }
       etemp=e;  }
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  /********************** nrerror ********************/
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {  void nrerror(char error_text[])
         d=p/q;  {
         u=x+d;    fprintf(stderr,"ERREUR ...\n");
         if (u-a < tol2 || b-u < tol2)    fprintf(stderr,"%s\n",error_text);
           d=SIGN(tol1,xm-x);    exit(EXIT_FAILURE);
       }  }
     } else {  /*********************** vector *******************/
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  double *vector(int nl, int nh)
     }  {
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    double *v;
     fu=(*f)(u);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (fu <= fx) {    if (!v) nrerror("allocation failure in vector");
       if (u >= x) a=x; else b=x;    return v-nl+NR_END;
       SHFT(v,w,x,u)  }
         SHFT(fv,fw,fx,fu)  
         } else {  /************************ free vector ******************/
           if (u < x) a=u; else b=u;  void free_vector(double*v, int nl, int nh)
           if (fu <= fw || w == x) {  {
             v=w;    free((FREE_ARG)(v+nl-NR_END));
             w=u;  }
             fv=fw;  
             fw=fu;  /************************ivector *******************************/
           } else if (fu <= fv || v == x || v == w) {  int *ivector(long nl,long nh)
             v=u;  {
             fv=fu;    int *v;
           }    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
         }    if (!v) nrerror("allocation failure in ivector");
   }    return v-nl+NR_END;
   nrerror("Too many iterations in brent");  }
   *xmin=x;  
   return fx;  /******************free ivector **************************/
 }  void free_ivector(int *v, long nl, long nh)
   {
 /****************** mnbrak ***********************/    free((FREE_ARG)(v+nl-NR_END));
   }
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))  /************************lvector *******************************/
 {  long *lvector(long nl,long nh)
   double ulim,u,r,q, dum;  {
   double fu;    long *v;
      v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   *fa=(*func)(*ax);    if (!v) nrerror("allocation failure in ivector");
   *fb=(*func)(*bx);    return v-nl+NR_END;
   if (*fb > *fa) {  }
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  /******************free lvector **************************/
       }  void free_lvector(long *v, long nl, long nh)
   *cx=(*bx)+GOLD*(*bx-*ax);  {
   *fc=(*func)(*cx);    free((FREE_ARG)(v+nl-NR_END));
   while (*fb > *fc) {  }
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);  /******************* imatrix *******************************/
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     ulim=(*bx)+GLIMIT*(*cx-*bx);  { 
     if ((*bx-u)*(u-*cx) > 0.0) {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       fu=(*func)(u);    int **m; 
     } else if ((*cx-u)*(u-ulim) > 0.0) {    
       fu=(*func)(u);    /* allocate pointers to rows */ 
       if (fu < *fc) {    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    if (!m) nrerror("allocation failure 1 in matrix()"); 
           SHFT(*fb,*fc,fu,(*func)(u))    m += NR_END; 
           }    m -= nrl; 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    
       u=ulim;    
       fu=(*func)(u);    /* allocate rows and set pointers to them */ 
     } else {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       u=(*cx)+GOLD*(*cx-*bx);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       fu=(*func)(u);    m[nrl] += NR_END; 
     }    m[nrl] -= ncl; 
     SHFT(*ax,*bx,*cx,u)    
       SHFT(*fa,*fb,*fc,fu)    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       }    
 }    /* return pointer to array of pointers to rows */ 
     return m; 
 /*************** linmin ************************/  } 
   
 int ncom;  /****************** free_imatrix *************************/
 double *pcom,*xicom;  void free_imatrix(m,nrl,nrh,ncl,nch)
 double (*nrfunc)(double []);        int **m;
          long nch,ncl,nrh,nrl; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))       /* free an int matrix allocated by imatrix() */ 
 {  { 
   double brent(double ax, double bx, double cx,    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
                double (*f)(double), double tol, double *xmin);    free((FREE_ARG) (m+nrl-NR_END)); 
   double f1dim(double x);  } 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));  /******************* matrix *******************************/
   int j;  double **matrix(long nrl, long nrh, long ncl, long nch)
   double xx,xmin,bx,ax;  {
   double fx,fb,fa;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
      double **m;
   ncom=n;  
   pcom=vector(1,n);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   xicom=vector(1,n);    if (!m) nrerror("allocation failure 1 in matrix()");
   nrfunc=func;    m += NR_END;
   for (j=1;j<=n;j++) {    m -= nrl;
     pcom[j]=p[j];  
     xicom[j]=xi[j];    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   ax=0.0;    m[nrl] += NR_END;
   xx=1.0;    m[nrl] -= ncl;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 #ifdef DEBUG    return m;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
 #endif     */
   for (j=1;j<=n;j++) {  }
     xi[j] *= xmin;  
     p[j] += xi[j];  /*************************free matrix ************************/
   }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   free_vector(xicom,1,n);  {
   free_vector(pcom,1,n);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 }    free((FREE_ARG)(m+nrl-NR_END));
   }
 /*************** powell ************************/  
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  /******************* ma3x *******************************/
             double (*func)(double []))  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 {  {
   void linmin(double p[], double xi[], int n, double *fret,    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
               double (*func)(double []));    double ***m;
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double fp,fptt;    if (!m) nrerror("allocation failure 1 in matrix()");
   double *xits;    m += NR_END;
   pt=vector(1,n);    m -= nrl;
   ptt=vector(1,n);  
   xit=vector(1,n);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   xits=vector(1,n);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   *fret=(*func)(p);    m[nrl] += NR_END;
   for (j=1;j<=n;j++) pt[j]=p[j];    m[nrl] -= ncl;
   for (*iter=1;;++(*iter)) {  
     fp=(*fret);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     ibig=0;  
     del=0.0;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     for (i=1;i<=n;i++)    m[nrl][ncl] += NR_END;
       printf(" %d %.12f",i, p[i]);    m[nrl][ncl] -= nll;
     printf("\n");    for (j=ncl+1; j<=nch; j++) 
     for (i=1;i<=n;i++) {      m[nrl][j]=m[nrl][j-1]+nlay;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    
       fptt=(*fret);    for (i=nrl+1; i<=nrh; i++) {
 #ifdef DEBUG      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       printf("fret=%lf \n",*fret);      for (j=ncl+1; j<=nch; j++) 
 #endif        m[i][j]=m[i][j-1]+nlay;
       printf("%d",i);fflush(stdout);    }
       linmin(p,xit,n,fret,func);    return m; 
       if (fabs(fptt-(*fret)) > del) {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         del=fabs(fptt-(*fret));             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
         ibig=i;    */
       }  }
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));  /*************************free ma3x ************************/
       for (j=1;j<=n;j++) {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  {
         printf(" x(%d)=%.12e",j,xit[j]);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       for(j=1;j<=n;j++)    free((FREE_ARG)(m+nrl-NR_END));
         printf(" p=%.12e",p[j]);  }
       printf("\n");  
 #endif  /*************** function subdirf ***********/
     }  char *subdirf(char fileres[])
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  {
 #ifdef DEBUG    /* Caution optionfilefiname is hidden */
       int k[2],l;    strcpy(tmpout,optionfilefiname);
       k[0]=1;    strcat(tmpout,"/"); /* Add to the right */
       k[1]=-1;    strcat(tmpout,fileres);
       printf("Max: %.12e",(*func)(p));    return tmpout;
       for (j=1;j<=n;j++)  }
         printf(" %.12e",p[j]);  
       printf("\n");  /*************** function subdirf2 ***********/
       for(l=0;l<=1;l++) {  char *subdirf2(char fileres[], char *preop)
         for (j=1;j<=n;j++) {  {
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    /* Caution optionfilefiname is hidden */
         }    strcpy(tmpout,optionfilefiname);
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    strcat(tmpout,"/");
       }    strcat(tmpout,preop);
 #endif    strcat(tmpout,fileres);
     return tmpout;
   }
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  /*************** function subdirf3 ***********/
       free_vector(ptt,1,n);  char *subdirf3(char fileres[], char *preop, char *preop2)
       free_vector(pt,1,n);  {
       return;    
     }    /* Caution optionfilefiname is hidden */
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    strcpy(tmpout,optionfilefiname);
     for (j=1;j<=n;j++) {    strcat(tmpout,"/");
       ptt[j]=2.0*p[j]-pt[j];    strcat(tmpout,preop);
       xit[j]=p[j]-pt[j];    strcat(tmpout,preop2);
       pt[j]=p[j];    strcat(tmpout,fileres);
     }    return tmpout;
     fptt=(*func)(ptt);  }
     if (fptt < fp) {  
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  /***************** f1dim *************************/
       if (t < 0.0) {  extern int ncom; 
         linmin(p,xit,n,fret,func);  extern double *pcom,*xicom;
         for (j=1;j<=n;j++) {  extern double (*nrfunc)(double []); 
           xi[j][ibig]=xi[j][n];   
           xi[j][n]=xit[j];  double f1dim(double x) 
         }  { 
 #ifdef DEBUG    int j; 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    double f;
         for(j=1;j<=n;j++)    double *xt; 
           printf(" %.12e",xit[j]);   
         printf("\n");    xt=vector(1,ncom); 
 #endif    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       }    f=(*nrfunc)(xt); 
     }    free_vector(xt,1,ncom); 
   }    return f; 
 }  } 
   
 /**** Prevalence limit ****************/  /*****************brent *************************/
   double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  { 
 {    int iter; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    double a,b,d,etemp;
      matrix by transitions matrix until convergence is reached */    double fu,fv,fw,fx;
     double ftemp;
   int i, ii,j,k;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   double min, max, maxmin, maxmax,sumnew=0.;    double e=0.0; 
   double **matprod2();   
   double **out, cov[NCOVMAX], **pmij();    a=(ax < cx ? ax : cx); 
   double **newm;    b=(ax > cx ? ax : cx); 
   double agefin, delaymax=50 ; /* Max number of years to converge */    x=w=v=bx; 
     fw=fv=fx=(*f)(x); 
   for (ii=1;ii<=nlstate+ndeath;ii++)    for (iter=1;iter<=ITMAX;iter++) { 
     for (j=1;j<=nlstate+ndeath;j++){      xm=0.5*(a+b); 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       printf(".");fflush(stdout);
    cov[1]=1.;      fprintf(ficlog,".");fflush(ficlog);
    #ifdef DEBUG
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      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);
     newm=savm;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     /* Covariates have to be included here again */  #endif
      cov[2]=agefin;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
          *xmin=x; 
       for (k=1; k<=cptcovn;k++) {        return fx; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      } 
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/      ftemp=fu;
       }      if (fabs(e) > tol1) { 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        r=(x-w)*(fx-fv); 
       for (k=1; k<=cptcovprod;k++)        q=(x-v)*(fx-fw); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        if (q > 0.0) p = -p; 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        q=fabs(q); 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/        etemp=e; 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);        e=d; 
         if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     savm=oldm;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     oldm=newm;        else { 
     maxmax=0.;          d=p/q; 
     for(j=1;j<=nlstate;j++){          u=x+d; 
       min=1.;          if (u-a < tol2 || b-u < tol2) 
       max=0.;            d=SIGN(tol1,xm-x); 
       for(i=1; i<=nlstate; i++) {        } 
         sumnew=0;      } else { 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         prlim[i][j]= newm[i][j]/(1-sumnew);      } 
         max=FMAX(max,prlim[i][j]);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         min=FMIN(min,prlim[i][j]);      fu=(*f)(u); 
       }      if (fu <= fx) { 
       maxmin=max-min;        if (u >= x) a=x; else b=x; 
       maxmax=FMAX(maxmax,maxmin);        SHFT(v,w,x,u) 
     }          SHFT(fv,fw,fx,fu) 
     if(maxmax < ftolpl){          } else { 
       return prlim;            if (u < x) a=u; else b=u; 
     }            if (fu <= fw || w == x) { 
   }              v=w; 
 }              w=u; 
               fv=fw; 
 /*************** transition probabilities ***************/              fw=fu; 
             } else if (fu <= fv || v == x || v == w) { 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )              v=u; 
 {              fv=fu; 
   double s1, s2;            } 
   /*double t34;*/          } 
   int i,j,j1, nc, ii, jj;    } 
     nrerror("Too many iterations in brent"); 
     for(i=1; i<= nlstate; i++){    *xmin=x; 
     for(j=1; j<i;j++){    return fx; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  } 
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  /****************** mnbrak ***********************/
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       ps[i][j]=s2;              double (*func)(double)) 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  { 
     }    double ulim,u,r,q, dum;
     for(j=i+1; j<=nlstate+ndeath;j++){    double fu; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){   
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    *fa=(*func)(*ax); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    *fb=(*func)(*bx); 
       }    if (*fb > *fa) { 
       ps[i][j]=s2;      SHFT(dum,*ax,*bx,dum) 
     }        SHFT(dum,*fb,*fa,dum) 
   }        } 
     /*ps[3][2]=1;*/    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
   for(i=1; i<= nlstate; i++){    while (*fb > *fc) { 
      s1=0;      r=(*bx-*ax)*(*fb-*fc); 
     for(j=1; j<i; j++)      q=(*bx-*cx)*(*fb-*fa); 
       s1+=exp(ps[i][j]);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     for(j=i+1; j<=nlstate+ndeath; j++)        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       s1+=exp(ps[i][j]);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     ps[i][i]=1./(s1+1.);      if ((*bx-u)*(u-*cx) > 0.0) { 
     for(j=1; j<i; j++)        fu=(*func)(u); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     for(j=i+1; j<=nlstate+ndeath; j++)        fu=(*func)(u); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        if (fu < *fc) { 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   } /* end i */            SHFT(*fb,*fc,fu,(*func)(u)) 
             } 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     for(jj=1; jj<= nlstate+ndeath; jj++){        u=ulim; 
       ps[ii][jj]=0;        fu=(*func)(u); 
       ps[ii][ii]=1;      } else { 
     }        u=(*cx)+GOLD*(*cx-*bx); 
   }        fu=(*func)(u); 
       } 
       SHFT(*ax,*bx,*cx,u) 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        SHFT(*fa,*fb,*fc,fu) 
     for(jj=1; jj<= nlstate+ndeath; jj++){        } 
      printf("%lf ",ps[ii][jj]);  } 
    }  
     printf("\n ");  /*************** linmin ************************/
     }  
     printf("\n ");printf("%lf ",cov[2]);*/  int ncom; 
 /*  double *pcom,*xicom;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  double (*nrfunc)(double []); 
   goto end;*/   
     return ps;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
 }  { 
     double brent(double ax, double bx, double cx, 
 /**************** Product of 2 matrices ******************/                 double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 {                double *fc, double (*func)(double)); 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    int j; 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    double xx,xmin,bx,ax; 
   /* in, b, out are matrice of pointers which should have been initialized    double fx,fb,fa;
      before: only the contents of out is modified. The function returns   
      a pointer to pointers identical to out */    ncom=n; 
   long i, j, k;    pcom=vector(1,n); 
   for(i=nrl; i<= nrh; i++)    xicom=vector(1,n); 
     for(k=ncolol; k<=ncoloh; k++)    nrfunc=func; 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    for (j=1;j<=n;j++) { 
         out[i][k] +=in[i][j]*b[j][k];      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
   return out;    } 
 }    ax=0.0; 
     xx=1.0; 
     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
 /************* Higher Matrix Product ***************/    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   #ifdef DEBUG
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 {    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  #endif
      duration (i.e. until    for (j=1;j<=n;j++) { 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      xi[j] *= xmin; 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      p[j] += xi[j]; 
      (typically every 2 years instead of every month which is too big).    } 
      Model is determined by parameters x and covariates have to be    free_vector(xicom,1,n); 
      included manually here.    free_vector(pcom,1,n); 
   } 
      */  
   char *asc_diff_time(long time_sec, char ascdiff[])
   int i, j, d, h, k;  {
   double **out, cov[NCOVMAX];    long sec_left, days, hours, minutes;
   double **newm;    days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
   /* Hstepm could be zero and should return the unit matrix */    hours = (sec_left) / (60*60) ;
   for (i=1;i<=nlstate+ndeath;i++)    sec_left = (sec_left) %(60*60);
     for (j=1;j<=nlstate+ndeath;j++){    minutes = (sec_left) /60;
       oldm[i][j]=(i==j ? 1.0 : 0.0);    sec_left = (sec_left) % (60);
       po[i][j][0]=(i==j ? 1.0 : 0.0);    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     }    return ascdiff;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  }
   for(h=1; h <=nhstepm; h++){  
     for(d=1; d <=hstepm; d++){  /*************** powell ************************/
       newm=savm;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       /* Covariates have to be included here again */              double (*func)(double [])) 
       cov[1]=1.;  { 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    void linmin(double p[], double xi[], int n, double *fret, 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];                double (*func)(double [])); 
       for (k=1; k<=cptcovage;k++)    int i,ibig,j; 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    double del,t,*pt,*ptt,*xit;
       for (k=1; k<=cptcovprod;k++)    double fp,fptt;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    double *xits;
     int niterf, itmp;
   
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    pt=vector(1,n); 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    ptt=vector(1,n); 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    xit=vector(1,n); 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    xits=vector(1,n); 
       savm=oldm;    *fret=(*func)(p); 
       oldm=newm;    for (j=1;j<=n;j++) pt[j]=p[j]; 
     }    for (*iter=1;;++(*iter)) { 
     for(i=1; i<=nlstate+ndeath; i++)      fp=(*fret); 
       for(j=1;j<=nlstate+ndeath;j++) {      ibig=0; 
         po[i][j][h]=newm[i][j];      del=0.0; 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      last_time=curr_time;
          */      (void) gettimeofday(&curr_time,&tzp);
       }      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
   } /* end h */      /*    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 po;      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]);
 /*************** log-likelihood *************/        fprintf(ficlog," %d %.12lf",i, p[i]);
 double func( double *x)        fprintf(ficrespow," %.12lf", p[i]);
 {      }
   int i, ii, j, k, mi, d, kk;      printf("\n");
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      fprintf(ficlog,"\n");
   double **out;      fprintf(ficrespow,"\n");fflush(ficrespow);
   double sw; /* Sum of weights */      if(*iter <=3){
   double lli; /* Individual log likelihood */        tm = *localtime(&curr_time.tv_sec);
   long ipmx;        strcpy(strcurr,asctime(&tm));
   /*extern weight */  /*       asctime_r(&tm,strcurr); */
   /* We are differentiating ll according to initial status */        forecast_time=curr_time; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        itmp = strlen(strcurr);
   /*for(i=1;i<imx;i++)        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     printf(" %d\n",s[4][i]);          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);
   cov[1]=1.;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         for(niterf=10;niterf<=30;niterf+=10){
   for(k=1; k<=nlstate; k++) ll[k]=0.;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){          tmf = *localtime(&forecast_time.tv_sec);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  /*      asctime_r(&tmf,strfor); */
     for(mi=1; mi<= wav[i]-1; mi++){          strcpy(strfor,asctime(&tmf));
       for (ii=1;ii<=nlstate+ndeath;ii++)          itmp = strlen(strfor);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          if(strfor[itmp-1]=='\n')
       for(d=0; d<dh[mi][i]; d++){          strfor[itmp-1]='\0';
         newm=savm;          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
         for (kk=1; kk<=cptcovage;kk++) {        }
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      }
         }      for (i=1;i<=n;i++) { 
                for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        fptt=(*fret); 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  #ifdef DEBUG
         savm=oldm;        printf("fret=%lf \n",*fret);
         oldm=newm;        fprintf(ficlog,"fret=%lf \n",*fret);
          #endif
                printf("%d",i);fflush(stdout);
       } /* end mult */        fprintf(ficlog,"%d",i);fflush(ficlog);
              linmin(p,xit,n,fret,func); 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        if (fabs(fptt-(*fret)) > del) { 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          del=fabs(fptt-(*fret)); 
       ipmx +=1;          ibig=i; 
       sw += weight[i];        } 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  #ifdef DEBUG
     } /* end of wave */        printf("%d %.12e",i,(*fret));
   } /* end of individual */        fprintf(ficlog,"%d %.12e",i,(*fret));
         for (j=1;j<=n;j++) {
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */          printf(" x(%d)=%.12e",j,xit[j]);
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   return -l;        }
 }        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[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;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   double fret;  #ifdef DEBUG
   xi=matrix(1,npar,1,npar);        int k[2],l;
   for (i=1;i<=npar;i++)        k[0]=1;
     for (j=1;j<=npar;j++)        k[1]=-1;
       xi[i][j]=(i==j ? 1.0 : 0.0);        printf("Max: %.12e",(*func)(p));
   printf("Powell\n");        fprintf(ficlog,"Max: %.12e",(*func)(p));
   powell(p,xi,npar,ftol,&iter,&fret,func);        for (j=1;j<=n;j++) {
           printf(" %.12e",p[j]);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          fprintf(ficlog," %.12e",p[j]);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        }
         printf("\n");
 }        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
 /**** Computes Hessian and covariance matrix ***/          for (j=1;j<=n;j++) {
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 {            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   double  **a,**y,*x,pd;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   double **hess;          }
   int i, j,jk;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   int *indx;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
   double hessii(double p[], double delta, int theta, double delti[]);  #endif
   double hessij(double p[], double delti[], int i, int j);  
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
   hess=matrix(1,npar,1,npar);        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
   printf("\nCalculation of the hessian matrix. Wait...\n");        return; 
   for (i=1;i<=npar;i++){      } 
     printf("%d",i);fflush(stdout);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     hess[i][i]=hessii(p,ftolhess,i,delti);      for (j=1;j<=n;j++) { 
     /*printf(" %f ",p[i]);*/        ptt[j]=2.0*p[j]-pt[j]; 
     /*printf(" %lf ",hess[i][i]);*/        xit[j]=p[j]-pt[j]; 
   }        pt[j]=p[j]; 
        } 
   for (i=1;i<=npar;i++) {      fptt=(*func)(ptt); 
     for (j=1;j<=npar;j++)  {      if (fptt < fp) { 
       if (j>i) {        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         printf(".%d%d",i,j);fflush(stdout);        if (t < 0.0) { 
         hess[i][j]=hessij(p,delti,i,j);          linmin(p,xit,n,fret,func); 
         hess[j][i]=hess[i][j];              for (j=1;j<=n;j++) { 
         /*printf(" %lf ",hess[i][j]);*/            xi[j][ibig]=xi[j][n]; 
       }            xi[j][n]=xit[j]; 
     }          }
   }  #ifdef DEBUG
   printf("\n");          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          for(j=1;j<=n;j++){
              printf(" %.12e",xit[j]);
   a=matrix(1,npar,1,npar);            fprintf(ficlog," %.12e",xit[j]);
   y=matrix(1,npar,1,npar);          }
   x=vector(1,npar);          printf("\n");
   indx=ivector(1,npar);          fprintf(ficlog,"\n");
   for (i=1;i<=npar;i++)  #endif
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        }
   ludcmp(a,npar,indx,&pd);      } 
     } 
   for (j=1;j<=npar;j++) {  } 
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  /**** Prevalence limit (stable prevalence)  ****************/
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       matcov[i][j]=x[i];  {
     }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   }       matrix by transitions matrix until convergence is reached */
   
   printf("\n#Hessian matrix#\n");    int i, ii,j,k;
   for (i=1;i<=npar;i++) {    double min, max, maxmin, maxmax,sumnew=0.;
     for (j=1;j<=npar;j++) {    double **matprod2();
       printf("%.3e ",hess[i][j]);    double **out, cov[NCOVMAX], **pmij();
     }    double **newm;
     printf("\n");    double agefin, delaymax=50 ; /* Max number of years to converge */
   }  
     for (ii=1;ii<=nlstate+ndeath;ii++)
   /* Recompute Inverse */      for (j=1;j<=nlstate+ndeath;j++){
   for (i=1;i<=npar;i++)        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      }
   ludcmp(a,npar,indx,&pd);  
      cov[1]=1.;
   /*  printf("\n#Hessian matrix recomputed#\n");   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for (j=1;j<=npar;j++) {    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     for (i=1;i<=npar;i++) x[i]=0;      newm=savm;
     x[j]=1;      /* Covariates have to be included here again */
     lubksb(a,npar,indx,x);       cov[2]=agefin;
     for (i=1;i<=npar;i++){    
       y[i][j]=x[i];        for (k=1; k<=cptcovn;k++) {
       printf("%.3e ",y[i][j]);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     }          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
     printf("\n");        }
   }        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   */        for (k=1; k<=cptcovprod;k++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   free_matrix(a,1,npar,1,npar);  
   free_matrix(y,1,npar,1,npar);        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   free_vector(x,1,npar);        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   free_ivector(indx,1,npar);        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   free_matrix(hess,1,npar,1,npar);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
       savm=oldm;
 }      oldm=newm;
       maxmax=0.;
 /*************** hessian matrix ****************/      for(j=1;j<=nlstate;j++){
 double hessii( double x[], double delta, int theta, double delti[])        min=1.;
 {        max=0.;
   int i;        for(i=1; i<=nlstate; i++) {
   int l=1, lmax=20;          sumnew=0;
   double k1,k2;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   double p2[NPARMAX+1];          prlim[i][j]= newm[i][j]/(1-sumnew);
   double res;          max=FMAX(max,prlim[i][j]);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          min=FMIN(min,prlim[i][j]);
   double fx;        }
   int k=0,kmax=10;        maxmin=max-min;
   double l1;        maxmax=FMAX(maxmax,maxmin);
       }
   fx=func(x);      if(maxmax < ftolpl){
   for (i=1;i<=npar;i++) p2[i]=x[i];        return prlim;
   for(l=0 ; l <=lmax; l++){      }
     l1=pow(10,l);    }
     delts=delt;  }
     for(k=1 ; k <kmax; k=k+1){  
       delt = delta*(l1*k);  /*************** transition probabilities ***************/ 
       p2[theta]=x[theta] +delt;  
       k1=func(p2)-fx;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       p2[theta]=x[theta]-delt;  {
       k2=func(p2)-fx;    double s1, s2;
       /*res= (k1-2.0*fx+k2)/delt/delt; */    /*double t34;*/
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    int i,j,j1, nc, ii, jj;
        
 #ifdef DEBUG      for(i=1; i<= nlstate; i++){
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        for(j=1; j<i;j++){
 #endif          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */            /*s2 += param[i][j][nc]*cov[nc];*/
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         k=kmax;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
       }          }
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          ps[i][j]=s2;
         k=kmax; l=lmax*10.;  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
       }        }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        for(j=i+1; j<=nlstate+ndeath;j++){
         delts=delt;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       }            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     }  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
   }          }
   delti[theta]=delts;          ps[i][j]=s2;
   return res;        }
        }
 }      /*ps[3][2]=1;*/
       
 double hessij( double x[], double delti[], int thetai,int thetaj)      for(i=1; i<= nlstate; i++){
 {        s1=0;
   int i;        for(j=1; j<i; j++)
   int l=1, l1, lmax=20;          s1+=exp(ps[i][j]);
   double k1,k2,k3,k4,res,fx;        for(j=i+1; j<=nlstate+ndeath; j++)
   double p2[NPARMAX+1];          s1+=exp(ps[i][j]);
   int k;        ps[i][i]=1./(s1+1.);
         for(j=1; j<i; j++)
   fx=func(x);          ps[i][j]= exp(ps[i][j])*ps[i][i];
   for (k=1; k<=2; k++) {        for(j=i+1; j<=nlstate+ndeath; j++)
     for (i=1;i<=npar;i++) p2[i]=x[i];          ps[i][j]= exp(ps[i][j])*ps[i][i];
     p2[thetai]=x[thetai]+delti[thetai]/k;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      } /* end i */
     k1=func(p2)-fx;      
        for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     p2[thetai]=x[thetai]+delti[thetai]/k;        for(jj=1; jj<= nlstate+ndeath; jj++){
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          ps[ii][jj]=0;
     k2=func(p2)-fx;          ps[ii][ii]=1;
          }
     p2[thetai]=x[thetai]-delti[thetai]/k;      }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      
     k3=func(p2)-fx;  
    /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
     p2[thetai]=x[thetai]-delti[thetai]/k;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  /*         printf("ddd %lf ",ps[ii][jj]); */
     k4=func(p2)-fx;  /*       } */
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  /*       printf("\n "); */
 #ifdef DEBUG  /*        } */
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  /*        printf("\n ");printf("%lf ",cov[2]); */
 #endif         /*
   }        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   return res;        goto end;*/
 }      return ps;
   }
 /************** Inverse of matrix **************/  
 void ludcmp(double **a, int n, int *indx, double *d)  /**************** Product of 2 matrices ******************/
 {  
   int i,imax,j,k;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   double big,dum,sum,temp;  {
   double *vv;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   vv=vector(1,n);    /* in, b, out are matrice of pointers which should have been initialized 
   *d=1.0;       before: only the contents of out is modified. The function returns
   for (i=1;i<=n;i++) {       a pointer to pointers identical to out */
     big=0.0;    long i, j, k;
     for (j=1;j<=n;j++)    for(i=nrl; i<= nrh; i++)
       if ((temp=fabs(a[i][j])) > big) big=temp;      for(k=ncolol; k<=ncoloh; k++)
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     vv[i]=1.0/big;          out[i][k] +=in[i][j]*b[j][k];
   }  
   for (j=1;j<=n;j++) {    return out;
     for (i=1;i<j;i++) {  }
       sum=a[i][j];  
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;  /************* Higher Matrix Product ***************/
     }  
     big=0.0;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     for (i=j;i<=n;i++) {  {
       sum=a[i][j];    /* Computes the transition matrix starting at age 'age' over 
       for (k=1;k<j;k++)       'nhstepm*hstepm*stepm' months (i.e. until
         sum -= a[i][k]*a[k][j];       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       a[i][j]=sum;       nhstepm*hstepm matrices. 
       if ( (dum=vv[i]*fabs(sum)) >= big) {       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         big=dum;       (typically every 2 years instead of every month which is too big 
         imax=i;       for the memory).
       }       Model is determined by parameters x and covariates have to be 
     }       included manually here. 
     if (j != imax) {  
       for (k=1;k<=n;k++) {       */
         dum=a[imax][k];  
         a[imax][k]=a[j][k];    int i, j, d, h, k;
         a[j][k]=dum;    double **out, cov[NCOVMAX];
       }    double **newm;
       *d = -(*d);  
       vv[imax]=vv[j];    /* Hstepm could be zero and should return the unit matrix */
     }    for (i=1;i<=nlstate+ndeath;i++)
     indx[j]=imax;      for (j=1;j<=nlstate+ndeath;j++){
     if (a[j][j] == 0.0) a[j][j]=TINY;        oldm[i][j]=(i==j ? 1.0 : 0.0);
     if (j != n) {        po[i][j][0]=(i==j ? 1.0 : 0.0);
       dum=1.0/(a[j][j]);      }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     }    for(h=1; h <=nhstepm; h++){
   }      for(d=1; d <=hstepm; d++){
   free_vector(vv,1,n);  /* Doesn't work */        newm=savm;
 ;        /* Covariates have to be included here again */
 }        cov[1]=1.;
         cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
 void lubksb(double **a, int n, int *indx, double b[])        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 {        for (k=1; k<=cptcovage;k++)
   int i,ii=0,ip,j;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double sum;        for (k=1; k<=cptcovprod;k++)
            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   for (i=1;i<=n;i++) {  
     ip=indx[i];  
     sum=b[ip];        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     b[ip]=b[i];        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     if (ii)        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     else if (sum) ii=i;        savm=oldm;
     b[i]=sum;        oldm=newm;
   }      }
   for (i=n;i>=1;i--) {      for(i=1; i<=nlstate+ndeath; i++)
     sum=b[i];        for(j=1;j<=nlstate+ndeath;j++) {
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          po[i][j][h]=newm[i][j];
     b[i]=sum/a[i][i];          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   }           */
 }        }
     } /* end h */
 /************ Frequencies ********************/    return po;
 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 */  
    
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  /*************** log-likelihood *************/
   double ***freq; /* Frequencies */  double func( double *x)
   double *pp;  {
   double pos, k2, dateintsum=0,k2cpt=0;    int i, ii, j, k, mi, d, kk;
   FILE *ficresp;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   char fileresp[FILENAMELENGTH];    double **out;
      double sw; /* Sum of weights */
   pp=vector(1,nlstate);    double lli; /* Individual log likelihood */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    int s1, s2;
   strcpy(fileresp,"p");    double bbh, survp;
   strcat(fileresp,fileres);    long ipmx;
   if((ficresp=fopen(fileresp,"w"))==NULL) {    /*extern weight */
     printf("Problem with prevalence resultfile: %s\n", fileresp);    /* We are differentiating ll according to initial status */
     exit(0);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   }    /*for(i=1;i<imx;i++) 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      printf(" %d\n",s[4][i]);
   j1=0;    */
      cov[1]=1.;
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    for(k=1; k<=nlstate; k++) ll[k]=0.;
    
   for(k1=1; k1<=j;k1++){    if(mle==1){
     for(i1=1; i1<=ncodemax[k1];i1++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       j1++;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        for(mi=1; mi<= wav[i]-1; mi++){
         scanf("%d", i);*/          for (ii=1;ii<=nlstate+ndeath;ii++)
       for (i=-1; i<=nlstate+ndeath; i++)              for (j=1;j<=nlstate+ndeath;j++){
         for (jk=-1; jk<=nlstate+ndeath; jk++)                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=agemin; m <= agemax+3; m++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             freq[i][jk][m]=0;            }
                for(d=0; d<dh[mi][i]; d++){
       dateintsum=0;            newm=savm;
       k2cpt=0;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for (i=1; i<=imx; i++) {            for (kk=1; kk<=cptcovage;kk++) {
         bool=1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         if  (cptcovn>0) {            }
           for (z1=1; z1<=cptcoveff; z1++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               bool=0;            savm=oldm;
         }            oldm=newm;
         if (bool==1) {          } /* end mult */
           for(m=firstpass; m<=lastpass; m++){        
             k2=anint[m][i]+(mint[m][i]/12.);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          /* But now since version 0.9 we anticipate for bias at large stepm.
               if(agev[m][i]==0) agev[m][i]=agemax+1;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
               if(agev[m][i]==1) agev[m][i]=agemax+2;           * (in months) between two waves is not a multiple of stepm, we rounded to 
               if (m<lastpass) {           * the nearest (and in case of equal distance, to the lowest) interval but now
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];           * we keep into memory the bias bh[mi][i] and also the previous matrix product
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
               }           * probability in order to take into account the bias as a fraction of the way
                         * from savm to out if bh is negative or even beyond if bh is positive. bh varies
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {           * -stepm/2 to stepm/2 .
                 dateintsum=dateintsum+k2;           * For stepm=1 the results are the same as for previous versions of Imach.
                 k2cpt++;           * For stepm > 1 the results are less biased than in previous versions. 
               }           */
             }          s1=s[mw[mi][i]][i];
           }          s2=s[mw[mi+1][i]][i];
         }          bbh=(double)bh[mi][i]/(double)stepm; 
       }          /* bias bh is positive if real duration
                   * is higher than the multiple of stepm and negative otherwise.
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);           */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       if  (cptcovn>0) {          if( s2 > nlstate){ 
         fprintf(ficresp, "\n#********** Variable ");            /* i.e. if s2 is a death state and if the date of death is known then the contribution
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);               to the likelihood is the probability to die between last step unit time and current 
         fprintf(ficresp, "**********\n#");               step unit time, which is also equal to probability to die before dh 
       }               minus probability to die before dh-stepm . 
       for(i=1; i<=nlstate;i++)               In version up to 0.92 likelihood was computed
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          as if date of death was unknown. Death was treated as any other
       fprintf(ficresp, "\n");          health state: the date of the interview describes the actual state
                and not the date of a change in health state. The former idea was
       for(i=(int)agemin; i <= (int)agemax+3; i++){          to consider that at each interview the state was recorded
         if(i==(int)agemax+3)          (healthy, disable or death) and IMaCh was corrected; but when we
           printf("Total");          introduced the exact date of death then we should have modified
         else          the contribution of an exact death to the likelihood. This new
           printf("Age %d", i);          contribution is smaller and very dependent of the step unit
         for(jk=1; jk <=nlstate ; jk++){          stepm. It is no more the probability to die between last interview
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          and month of death but the probability to survive from last
             pp[jk] += freq[jk][m][i];          interview up to one month before death multiplied by the
         }          probability to die within a month. Thanks to Chris
         for(jk=1; jk <=nlstate ; jk++){          Jackson for correcting this bug.  Former versions increased
           for(m=-1, pos=0; m <=0 ; m++)          mortality artificially. The bad side is that we add another loop
             pos += freq[jk][m][i];          which slows down the processing. The difference can be up to 10%
           if(pp[jk]>=1.e-10)          lower mortality.
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            */
           else            lli=log(out[s1][s2] - savm[s1][s2]);
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          }else{
         }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
         for(jk=1; jk <=nlstate ; jk++){          } 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
             pp[jk] += freq[jk][m][i];          /*if(lli ==000.0)*/
         }          /*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); */
           ipmx +=1;
         for(jk=1,pos=0; jk <=nlstate ; jk++)          sw += weight[i];
           pos += pp[jk];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for(jk=1; jk <=nlstate ; jk++){        } /* end of wave */
           if(pos>=1.e-5)      } /* end of individual */
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    }  else if(mle==2){
           else      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           if( i <= (int) agemax){        for(mi=1; mi<= wav[i]-1; mi++){
             if(pos>=1.e-5){          for (ii=1;ii<=nlstate+ndeath;ii++)
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            for (j=1;j<=nlstate+ndeath;j++){
               probs[i][jk][j1]= pp[jk]/pos;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }            }
             else          for(d=0; d<=dh[mi][i]; d++){
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            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];
         for(jk=-1; jk <=nlstate+ndeath; jk++)            }
           for(m=-1; m <=nlstate+ndeath; m++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if(i <= (int) agemax)            savm=oldm;
           fprintf(ficresp,"\n");            oldm=newm;
         printf("\n");          } /* end mult */
       }        
     }          s1=s[mw[mi][i]][i];
   }          s2=s[mw[mi+1][i]][i];
   dateintmean=dateintsum/k2cpt;          bbh=(double)bh[mi][i]/(double)stepm; 
            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 */
   fclose(ficresp);          ipmx +=1;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          sw += weight[i];
   free_vector(pp,1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
   /* End of Freq */      } /* end of individual */
 }    }  else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 /************ Prevalence ********************/        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 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)        for(mi=1; mi<= wav[i]-1; mi++){
 {  /* Some frequencies */          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double ***freq; /* Frequencies */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double *pp;            }
   double pos, k2;          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   pp=vector(1,nlstate);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            }
   j1=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   j=cptcoveff;            savm=oldm;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            oldm=newm;
            } /* end mult */
   for(k1=1; k1<=j;k1++){        
     for(i1=1; i1<=ncodemax[k1];i1++){          s1=s[mw[mi][i]][i];
       j1++;          s2=s[mw[mi+1][i]][i];
                bbh=(double)bh[mi][i]/(double)stepm; 
       for (i=-1; i<=nlstate+ndeath; i++)            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+ndeath; jk++)            ipmx +=1;
           for(m=agemin; m <= agemax+3; m++)          sw += weight[i];
             freq[i][jk][m]=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
              } /* end of wave */
       for (i=1; i<=imx; i++) {      } /* end of individual */
         bool=1;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
         if  (cptcovn>0) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           for (z1=1; z1<=cptcoveff; z1++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        for(mi=1; mi<= wav[i]-1; mi++){
               bool=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
         }            for (j=1;j<=nlstate+ndeath;j++){
         if (bool==1) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=firstpass; m<=lastpass; m++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             k2=anint[m][i]+(mint[m][i]/12.);            }
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          for(d=0; d<dh[mi][i]; d++){
               if(agev[m][i]==0) agev[m][i]=agemax+1;            newm=savm;
               if(agev[m][i]==1) agev[m][i]=agemax+2;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
               if (m<lastpass) {            for (kk=1; kk<=cptcovage;kk++) {
                 if (calagedate>0)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                   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];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               }            savm=oldm;
             }            oldm=newm;
           }          } /* end mult */
         }        
       }          s1=s[mw[mi][i]][i];
       for(i=(int)agemin; i <= (int)agemax+3; i++){          s2=s[mw[mi+1][i]][i];
         for(jk=1; jk <=nlstate ; jk++){          if( s2 > nlstate){ 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            lli=log(out[s1][s2] - savm[s1][s2]);
             pp[jk] += freq[jk][m][i];          }else{
         }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         for(jk=1; jk <=nlstate ; jk++){          }
           for(m=-1, pos=0; m <=0 ; m++)          ipmx +=1;
             pos += freq[jk][m][i];          sw += weight[i];
         }          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]); */
         for(jk=1; jk <=nlstate ; jk++){        } /* end of wave */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      } /* end of individual */
             pp[jk] += freq[jk][m][i];    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
         }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        for(mi=1; mi<= wav[i]-1; mi++){
                  for (ii=1;ii<=nlstate+ndeath;ii++)
         for(jk=1; jk <=nlstate ; jk++){                for (j=1;j<=nlstate+ndeath;j++){
           if( i <= (int) agemax){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             if(pos>=1.e-5){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
               probs[i][jk][j1]= pp[jk]/pos;            }
             }          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];
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          ipmx +=1;
 {          sw += weight[i];
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      Death is a valid wave (if date is known).          /*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]);*/
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        } /* end of wave */
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      } /* end of individual */
      and mw[mi+1][i]. dh depends on stepm.    } /* End of if */
      */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   int i, mi, m;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    return -l;
      double sum=0., jmean=0.;*/  }
   
   int j, k=0,jk, ju, jl;  /*************** log-likelihood *************/
   double sum=0.;  double funcone( double *x)
   jmin=1e+5;  {
   jmax=-1;    /* Same as likeli but slower because of a lot of printf and if */
   jmean=0.;    int i, ii, j, k, mi, d, kk;
   for(i=1; i<=imx; i++){    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     mi=0;    double **out;
     m=firstpass;    double lli; /* Individual log likelihood */
     while(s[m][i] <= nlstate){    double llt;
       if(s[m][i]>=1)    int s1, s2;
         mw[++mi][i]=m;    double bbh, survp;
       if(m >=lastpass)    /*extern weight */
         break;    /* We are differentiating ll according to initial status */
       else    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         m++;    /*for(i=1;i<imx;i++) 
     }/* end while */      printf(" %d\n",s[4][i]);
     if (s[m][i] > nlstate){    */
       mi++;     /* Death is another wave */    cov[1]=1.;
       /* if(mi==0)  never been interviewed correctly before death */  
          /* Only death is a correct wave */    for(k=1; k<=nlstate; k++) ll[k]=0.;
       mw[mi][i]=m;  
     }    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     wav[i]=mi;      for(mi=1; mi<= wav[i]-1; mi++){
     if(mi==0)        for (ii=1;ii<=nlstate+ndeath;ii++)
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          for (j=1;j<=nlstate+ndeath;j++){
   }            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for(i=1; i<=imx; i++){          }
     for(mi=1; mi<wav[i];mi++){        for(d=0; d<dh[mi][i]; d++){
       if (stepm <=0)          newm=savm;
         dh[mi][i]=1;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       else{          for (kk=1; kk<=cptcovage;kk++) {
         if (s[mw[mi+1][i]][i] > nlstate) {            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           if (agedc[i] < 2*AGESUP) {          }
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           if(j==0) j=1;  /* Survives at least one month after exam */                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           k=k+1;          savm=oldm;
           if (j >= jmax) jmax=j;          oldm=newm;
           if (j <= jmin) jmin=j;        } /* end mult */
           sum=sum+j;        
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        s1=s[mw[mi][i]][i];
           }        s2=s[mw[mi+1][i]][i];
         }        bbh=(double)bh[mi][i]/(double)stepm; 
         else{        /* bias is positive if real duration
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));         * is higher than the multiple of stepm and negative otherwise.
           k=k+1;         */
           if (j >= jmax) jmax=j;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           else if (j <= jmin)jmin=j;          lli=log(out[s1][s2] - savm[s1][s2]);
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        } else if (mle==1){
           sum=sum+j;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         }        } else if(mle==2){
         jk= j/stepm;          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 */
         jl= j -jk*stepm;        } else if(mle==3){  /* exponential inter-extrapolation */
         ju= j -(jk+1)*stepm;          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 */
         if(jl <= -ju)        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           dh[mi][i]=jk;          lli=log(out[s1][s2]); /* Original formula */
         else        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           dh[mi][i]=jk+1;          lli=log(out[s1][s2]); /* Original formula */
         if(dh[mi][i]==0)        } /* End of if */
           dh[mi][i]=1; /* At least one step */        ipmx +=1;
       }        sw += weight[i];
     }        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]); */
   jmean=sum/k;        if(globpr){
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
  }   %10.6f %10.6f %10.6f ", \
 /*********** Tricode ****************************/                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
 void tricode(int *Tvar, int **nbcode, int imx)                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
 {          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   int Ndum[20],ij=1, k, j, i;            llt +=ll[k]*gipmx/gsw;
   int cptcode=0;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   cptcoveff=0;          }
            fprintf(ficresilk," %10.6f\n", -llt);
   for (k=0; k<19; k++) Ndum[k]=0;        }
   for (k=1; k<=7; k++) ncodemax[k]=0;      } /* end of wave */
     } /* end of individual */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     for (i=1; i<=imx; i++) {    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       ij=(int)(covar[Tvar[j]][i]);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       Ndum[ij]++;    if(globpr==0){ /* First time we count the contributions and weights */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      gipmx=ipmx;
       if (ij > cptcode) cptcode=ij;      gsw=sw;
     }    }
     return -l;
     for (i=0; i<=cptcode; i++) {  }
       if(Ndum[i]!=0) ncodemax[j]++;  
     }  
     ij=1;  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   {
     for (i=1; i<=ncodemax[j]; i++) {    /* This routine should help understanding what is done with 
       for (k=0; k<=19; k++) {       the selection of individuals/waves and
         if (Ndum[k] != 0) {       to check the exact contribution to the likelihood.
           nbcode[Tvar[j]][ij]=k;       Plotting could be done.
               */
           ij++;    int k;
         }  
         if (ij > ncodemax[j]) break;    if(*globpri !=0){ /* Just counts and sums, no printings */
       }        strcpy(fileresilk,"ilk"); 
     }      strcat(fileresilk,fileres);
   }        if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
  for (k=0; k<19; k++) Ndum[k]=0;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
  for (i=1; i<=ncovmodel-2; i++) {      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");
       ij=Tvar[i];      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       Ndum[ij]++;      /*  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++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
  ij=1;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
  for (i=1; i<=10; i++) {    }
    if((Ndum[i]!=0) && (i<=ncovcol)){  
      Tvaraff[ij]=i;    *fretone=(*funcone)(p);
      ij++;    if(*globpri !=0){
    }      fclose(ficresilk);
  }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
        fflush(fichtm); 
     cptcoveff=ij-1;    } 
 }    return;
   }
 /*********** Health Expectancies ****************/  
   
 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 )  /*********** Maximum Likelihood Estimation ***************/
   
 {  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   /* Health expectancies */  {
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;    int i,j, iter;
   double age, agelim, hf;    double **xi;
   double ***p3mat,***varhe;    double fret;
   double **dnewm,**doldm;    double fretone; /* Only one call to likelihood */
   double *xp;    /*  char filerespow[FILENAMELENGTH];*/
   double **gp, **gm;    xi=matrix(1,npar,1,npar);
   double ***gradg, ***trgradg;    for (i=1;i<=npar;i++)
   int theta;      for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   xp=vector(1,npar);    strcpy(filerespow,"pow"); 
   dnewm=matrix(1,nlstate*2,1,npar);    strcat(filerespow,fileres);
   doldm=matrix(1,nlstate*2,1,nlstate*2);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", filerespow);
   fprintf(ficreseij,"# Health expectancies\n");      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   fprintf(ficreseij,"# Age");    }
   for(i=1; i<=nlstate;i++)    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for(j=1; j<=nlstate;j++)    for (i=1;i<=nlstate;i++)
       fprintf(ficreseij," %1d-%1d (SE)",i,j);      for(j=1;j<=nlstate+ndeath;j++)
   fprintf(ficreseij,"\n");        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fprintf(ficrespow,"\n");
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);    powell(p,xi,npar,ftol,&iter,&fret,func);
   }  
   else  hstepm=estepm;      fclose(ficrespow);
   /* We compute the life expectancy from trapezoids spaced every estepm months    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
    * This is mainly to measure the difference between two models: for example    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
    * if stepm=24 months pijx are given only every 2 years and by summing them    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
    * we are calculating an estimate of the Life Expectancy assuming a linear  
    * progression inbetween and thus overestimating or underestimating according  }
    * 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  /**** Computes Hessian and covariance matrix ***/
    * to compare the new estimate of Life expectancy with the same linear  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
    * hypothesis. A more precise result, taking into account a more precise  {
    * curvature will be obtained if estepm is as small as stepm. */    double  **a,**y,*x,pd;
     double **hess;
   /* For example we decided to compute the life expectancy with the smallest unit */    int i, j,jk;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    int *indx;
      nhstepm is the number of hstepm from age to agelim  
      nstepm is the number of stepm from age to agelin.    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
      Look at hpijx to understand the reason of that which relies in memory size    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
      and note for a fixed period like estepm months */    void lubksb(double **a, int npar, int *indx, double b[]) ;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    void ludcmp(double **a, int npar, int *indx, double *d) ;
      survival function given by stepm (the optimization length). Unfortunately it    double gompertz(double p[]);
      means that if the survival funtion is printed only each two years of age and if    hess=matrix(1,npar,1,npar);
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  
      results. So we changed our mind and took the option of the best precision.    printf("\nCalculation of the hessian matrix. Wait...\n");
   */    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    for (i=1;i<=npar;i++){
       printf("%d",i);fflush(stdout);
   agelim=AGESUP;      fprintf(ficlog,"%d",i);fflush(ficlog);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */     
     /* nhstepm age range expressed in number of stepm */       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */      /*  printf(" %f ",p[i]);
     /* if (stepm >= YEARM) hstepm=1;*/          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    for (i=1;i<=npar;i++) {
     gp=matrix(0,nhstepm,1,nlstate*2);      for (j=1;j<=npar;j++)  {
     gm=matrix(0,nhstepm,1,nlstate*2);        if (j>i) { 
           printf(".%d%d",i,j);fflush(stdout);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          hess[i][j]=hessij(p,delti,i,j,func,npar);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            
            hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        }
       }
     /* Computing Variances of health expectancies */    }
     printf("\n");
      for(theta=1; theta <=npar; theta++){    fprintf(ficlog,"\n");
       for(i=1; i<=npar; i++){  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      
      a=matrix(1,npar,1,npar);
       cptj=0;    y=matrix(1,npar,1,npar);
       for(j=1; j<= nlstate; j++){    x=vector(1,npar);
         for(i=1; i<=nlstate; i++){    indx=ivector(1,npar);
           cptj=cptj+1;    for (i=1;i<=npar;i++)
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    ludcmp(a,npar,indx,&pd);
           }  
         }    for (j=1;j<=npar;j++) {
       }      for (i=1;i<=npar;i++) x[i]=0;
            x[j]=1;
            lubksb(a,npar,indx,x);
       for(i=1; i<=npar; i++)      for (i=1;i<=npar;i++){ 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        matcov[i][j]=x[i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        }
          }
       cptj=0;  
       for(j=1; j<= nlstate; j++){    printf("\n#Hessian matrix#\n");
         for(i=1;i<=nlstate;i++){    fprintf(ficlog,"\n#Hessian matrix#\n");
           cptj=cptj+1;    for (i=1;i<=npar;i++) { 
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){      for (j=1;j<=npar;j++) { 
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        printf("%.3e ",hess[i][j]);
           }        fprintf(ficlog,"%.3e ",hess[i][j]);
         }      }
       }      printf("\n");
       for(j=1; j<= nlstate*2; j++)      fprintf(ficlog,"\n");
         for(h=0; h<=nhstepm-1; h++){    }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  
         }    /* Recompute Inverse */
      }    for (i=1;i<=npar;i++)
          for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
 /* End theta */    ludcmp(a,npar,indx,&pd);
   
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    /*  printf("\n#Hessian matrix recomputed#\n");
   
      for(h=0; h<=nhstepm-1; h++)    for (j=1;j<=npar;j++) {
       for(j=1; j<=nlstate*2;j++)      for (i=1;i<=npar;i++) x[i]=0;
         for(theta=1; theta <=npar; theta++)      x[j]=1;
           trgradg[h][j][theta]=gradg[h][theta][j];      lubksb(a,npar,indx,x);
            for (i=1;i<=npar;i++){ 
         y[i][j]=x[i];
      for(i=1;i<=nlstate*2;i++)        printf("%.3e ",y[i][j]);
       for(j=1;j<=nlstate*2;j++)        fprintf(ficlog,"%.3e ",y[i][j]);
         varhe[i][j][(int)age] =0.;      }
       printf("\n");
      printf("%d|",(int)age);fflush(stdout);      fprintf(ficlog,"\n");
      for(h=0;h<=nhstepm-1;h++){    }
       for(k=0;k<=nhstepm-1;k++){    */
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);  
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);    free_matrix(a,1,npar,1,npar);
         for(i=1;i<=nlstate*2;i++)    free_matrix(y,1,npar,1,npar);
           for(j=1;j<=nlstate*2;j++)    free_vector(x,1,npar);
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    free_ivector(indx,1,npar);
       }    free_matrix(hess,1,npar,1,npar);
     }  
     /* Computing expectancies */  
     for(i=1; i<=nlstate;i++)  }
       for(j=1; j<=nlstate;j++)  
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){  /*************** hessian matrix ****************/
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
            {
 /* 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]);*/    int i;
     int l=1, lmax=20;
         }    double k1,k2;
     double p2[NPARMAX+1];
     fprintf(ficreseij,"%3.0f",age );    double res;
     cptj=0;    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     for(i=1; i<=nlstate;i++)    double fx;
       for(j=1; j<=nlstate;j++){    int k=0,kmax=10;
         cptj++;    double l1;
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );  
       }    fx=func(x);
     fprintf(ficreseij,"\n");    for (i=1;i<=npar;i++) p2[i]=x[i];
        for(l=0 ; l <=lmax; l++){
     free_matrix(gm,0,nhstepm,1,nlstate*2);      l1=pow(10,l);
     free_matrix(gp,0,nhstepm,1,nlstate*2);      delts=delt;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);      for(k=1 ; k <kmax; k=k+1){
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);        delt = delta*(l1*k);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        p2[theta]=x[theta] +delt;
   }        k1=func(p2)-fx;
   printf("\n");        p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
   free_vector(xp,1,npar);        /*res= (k1-2.0*fx+k2)/delt/delt; */
   free_matrix(dnewm,1,nlstate*2,1,npar);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);        
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);  #ifdef DEBUG
 }        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         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);
 /************ Variance ******************/  #endif
 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)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
 {        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   /* Variance of health expectancies */          k=kmax;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        }
   double **newm;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   double **dnewm,**doldm;          k=kmax; l=lmax*10.;
   int i, j, nhstepm, hstepm, h, nstepm ;        }
   int k, cptcode;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   double *xp;          delts=delt;
   double **gp, **gm;        }
   double ***gradg, ***trgradg;      }
   double ***p3mat;    }
   double age,agelim, hf;    delti[theta]=delts;
   int theta;    return res; 
     
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");  }
   fprintf(ficresvij,"# Age");  
   for(i=1; i<=nlstate;i++)  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     for(j=1; j<=nlstate;j++)  {
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    int i;
   fprintf(ficresvij,"\n");    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
   xp=vector(1,npar);    double p2[NPARMAX+1];
   dnewm=matrix(1,nlstate,1,npar);    int k;
   doldm=matrix(1,nlstate,1,nlstate);  
      fx=func(x);
   if(estepm < stepm){    for (k=1; k<=2; k++) {
     printf ("Problem %d lower than %d\n",estepm, stepm);      for (i=1;i<=npar;i++) p2[i]=x[i];
   }      p2[thetai]=x[thetai]+delti[thetai]/k;
   else  hstepm=estepm;        p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   /* For example we decided to compute the life expectancy with the smallest unit */      k1=func(p2)-fx;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    
      nhstepm is the number of hstepm from age to agelim      p2[thetai]=x[thetai]+delti[thetai]/k;
      nstepm is the number of stepm from age to agelin.      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
      Look at hpijx to understand the reason of that which relies in memory size      k2=func(p2)-fx;
      and note for a fixed period like k years */    
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      p2[thetai]=x[thetai]-delti[thetai]/k;
      survival function given by stepm (the optimization length). Unfortunately it      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
      means that if the survival funtion is printed only each two years of age and if      k3=func(p2)-fx;
      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.      p2[thetai]=x[thetai]-delti[thetai]/k;
   */      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      k4=func(p2)-fx;
   agelim = AGESUP;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  #ifdef DEBUG
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      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);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  #endif
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    }
     gp=matrix(0,nhstepm,1,nlstate);    return res;
     gm=matrix(0,nhstepm,1,nlstate);  }
   
     for(theta=1; theta <=npar; theta++){  /************** Inverse of matrix **************/
       for(i=1; i<=npar; i++){ /* Computes gradient */  void ludcmp(double **a, int n, int *indx, double *d) 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  { 
       }    int i,imax,j,k; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      double big,dum,sum,temp; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double *vv; 
    
       if (popbased==1) {    vv=vector(1,n); 
         for(i=1; i<=nlstate;i++)    *d=1.0; 
           prlim[i][i]=probs[(int)age][i][ij];    for (i=1;i<=n;i++) { 
       }      big=0.0; 
        for (j=1;j<=n;j++) 
       for(j=1; j<= nlstate; j++){        if ((temp=fabs(a[i][j])) > big) big=temp; 
         for(h=0; h<=nhstepm; h++){      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      vv[i]=1.0/big; 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    } 
         }    for (j=1;j<=n;j++) { 
       }      for (i=1;i<j;i++) { 
            sum=a[i][j]; 
       for(i=1; i<=npar; i++) /* Computes gradient */        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        a[i][j]=sum; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        } 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      big=0.0; 
        for (i=j;i<=n;i++) { 
       if (popbased==1) {        sum=a[i][j]; 
         for(i=1; i<=nlstate;i++)        for (k=1;k<j;k++) 
           prlim[i][i]=probs[(int)age][i][ij];          sum -= a[i][k]*a[k][j]; 
       }        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
       for(j=1; j<= nlstate; j++){          big=dum; 
         for(h=0; h<=nhstepm; h++){          imax=i; 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        } 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      } 
         }      if (j != imax) { 
       }        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
       for(j=1; j<= nlstate; j++)          a[imax][k]=a[j][k]; 
         for(h=0; h<=nhstepm; h++){          a[j][k]=dum; 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        } 
         }        *d = -(*d); 
     } /* End theta */        vv[imax]=vv[j]; 
       } 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
     for(h=0; h<=nhstepm; h++)      if (j != n) { 
       for(j=1; j<=nlstate;j++)        dum=1.0/(a[j][j]); 
         for(theta=1; theta <=npar; theta++)        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
           trgradg[h][j][theta]=gradg[h][theta][j];      } 
     } 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    free_vector(vv,1,n);  /* Doesn't work */
     for(i=1;i<=nlstate;i++)  ;
       for(j=1;j<=nlstate;j++)  } 
         vareij[i][j][(int)age] =0.;  
   void lubksb(double **a, int n, int *indx, double b[]) 
     for(h=0;h<=nhstepm;h++){  { 
       for(k=0;k<=nhstepm;k++){    int i,ii=0,ip,j; 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    double sum; 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);   
         for(i=1;i<=nlstate;i++)    for (i=1;i<=n;i++) { 
           for(j=1;j<=nlstate;j++)      ip=indx[i]; 
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;      sum=b[ip]; 
       }      b[ip]=b[i]; 
     }      if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     fprintf(ficresvij,"%.0f ",age );      else if (sum) ii=i; 
     for(i=1; i<=nlstate;i++)      b[i]=sum; 
       for(j=1; j<=nlstate;j++){    } 
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    for (i=n;i>=1;i--) { 
       }      sum=b[i]; 
     fprintf(ficresvij,"\n");      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     free_matrix(gp,0,nhstepm,1,nlstate);      b[i]=sum/a[i][i]; 
     free_matrix(gm,0,nhstepm,1,nlstate);    } 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  } 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /************ Frequencies ********************/
   } /* End age */  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 */
   free_vector(xp,1,npar);    
   free_matrix(doldm,1,nlstate,1,npar);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   free_matrix(dnewm,1,nlstate,1,nlstate);    int first;
     double ***freq; /* Frequencies */
 }    double *pp, **prop;
     double pos,posprop, k2, dateintsum=0,k2cpt=0;
 /************ Variance of prevlim ******************/    FILE *ficresp;
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    char fileresp[FILENAMELENGTH];
 {    
   /* Variance of prevalence limit */    pp=vector(1,nlstate);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    prop=matrix(1,nlstate,iagemin,iagemax+3);
   double **newm;    strcpy(fileresp,"p");
   double **dnewm,**doldm;    strcat(fileresp,fileres);
   int i, j, nhstepm, hstepm;    if((ficresp=fopen(fileresp,"w"))==NULL) {
   int k, cptcode;      printf("Problem with prevalence resultfile: %s\n", fileresp);
   double *xp;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   double *gp, *gm;      exit(0);
   double **gradg, **trgradg;    }
   double age,agelim;    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
   int theta;    j1=0;
        
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");    j=cptcoveff;
   fprintf(ficresvpl,"# Age");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %1d-%1d",i,i);    first=1;
   fprintf(ficresvpl,"\n");  
     for(k1=1; k1<=j;k1++){
   xp=vector(1,npar);      for(i1=1; i1<=ncodemax[k1];i1++){
   dnewm=matrix(1,nlstate,1,npar);        j1++;
   doldm=matrix(1,nlstate,1,nlstate);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
            scanf("%d", i);*/
   hstepm=1*YEARM; /* Every year of age */        for (i=-1; i<=nlstate+ndeath; i++)  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   agelim = AGESUP;            for(m=iagemin; m <= iagemax+3; m++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              freq[i][jk][m]=0;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
     if (stepm >= YEARM) hstepm=1;      for (i=1; i<=nlstate; i++)  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        for(m=iagemin; m <= iagemax+3; m++)
     gradg=matrix(1,npar,1,nlstate);          prop[i][m]=0;
     gp=vector(1,nlstate);        
     gm=vector(1,nlstate);        dateintsum=0;
         k2cpt=0;
     for(theta=1; theta <=npar; theta++){        for (i=1; i<=imx; i++) {
       for(i=1; i<=npar; i++){ /* Computes gradient */          bool=1;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          if  (cptcovn>0) {
       }            for (z1=1; z1<=cptcoveff; z1++) 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       for(i=1;i<=nlstate;i++)                bool=0;
         gp[i] = prlim[i][i];          }
              if (bool==1){
       for(i=1; i<=npar; i++) /* Computes gradient */            for(m=firstpass; m<=lastpass; m++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              k2=anint[m][i]+(mint[m][i]/12.);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       for(i=1;i<=nlstate;i++)                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         gm[i] = prlim[i][i];                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       for(i=1;i<=nlstate;i++)                if (m<lastpass) {
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     } /* End theta */                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                 }
     trgradg =matrix(1,nlstate,1,npar);                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     for(j=1; j<=nlstate;j++)                  dateintsum=dateintsum+k2;
       for(theta=1; theta <=npar; theta++)                  k2cpt++;
         trgradg[j][theta]=gradg[theta][j];                }
                 /*}*/
     for(i=1;i<=nlstate;i++)            }
       varpl[i][(int)age] =0.;          }
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        }
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);         
     for(i=1;i<=nlstate;i++)        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  
         if  (cptcovn>0) {
     fprintf(ficresvpl,"%.0f ",age );          fprintf(ficresp, "\n#********** Variable "); 
     for(i=1; i<=nlstate;i++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          fprintf(ficresp, "**********\n#");
     fprintf(ficresvpl,"\n");        }
     free_vector(gp,1,nlstate);        for(i=1; i<=nlstate;i++) 
     free_vector(gm,1,nlstate);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     free_matrix(gradg,1,npar,1,nlstate);        fprintf(ficresp, "\n");
     free_matrix(trgradg,1,nlstate,1,npar);        
   } /* End age */        for(i=iagemin; i <= iagemax+3; i++){
           if(i==iagemax+3){
   free_vector(xp,1,npar);            fprintf(ficlog,"Total");
   free_matrix(doldm,1,nlstate,1,npar);          }else{
   free_matrix(dnewm,1,nlstate,1,nlstate);            if(first==1){
               first=0;
 }              printf("See log file for details...\n");
             }
 /************ Variance of one-step probabilities  ******************/            fprintf(ficlog,"Age %d", i);
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)          }
 {          for(jk=1; jk <=nlstate ; jk++){
   int i, j,  i1, k1, l1;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   int k2, l2, j1,  z1;              pp[jk] += freq[jk][m][i]; 
   int k=0,l, cptcode;          }
   int first=1;          for(jk=1; jk <=nlstate ; jk++){
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;            for(m=-1, pos=0; m <=0 ; m++)
   double **dnewm,**doldm;              pos += freq[jk][m][i];
   double *xp;            if(pp[jk]>=1.e-10){
   double *gp, *gm;              if(first==1){
   double **gradg, **trgradg;              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   double **mu;              }
   double age,agelim, cov[NCOVMAX];              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */            }else{
   int theta;              if(first==1)
   char fileresprob[FILENAMELENGTH];                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   char fileresprobcov[FILENAMELENGTH];              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   char fileresprobcor[FILENAMELENGTH];            }
           }
   double ***varpij;  
           for(jk=1; jk <=nlstate ; jk++){
   strcpy(fileresprob,"prob");            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   strcat(fileresprob,fileres);              pp[jk] += freq[jk][m][i];
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          }       
     printf("Problem with resultfile: %s\n", fileresprob);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   }            pos += pp[jk];
   strcpy(fileresprobcov,"probcov");            posprop += prop[jk][i];
   strcat(fileresprobcov,fileres);          }
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {          for(jk=1; jk <=nlstate ; jk++){
     printf("Problem with resultfile: %s\n", fileresprobcov);            if(pos>=1.e-5){
   }              if(first==1)
   strcpy(fileresprobcor,"probcor");                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   strcat(fileresprobcor,fileres);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {            }else{
     printf("Problem with resultfile: %s\n", fileresprobcor);              if(first==1)
   }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   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);            if( i <= iagemax){
                if(pos>=1.e-5){
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   fprintf(ficresprob,"# Age");                /*probs[i][jk][j1]= pp[jk]/pos;*/
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");                /*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(ficresprobcov,"# Age");              }
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");              else
   fprintf(ficresprobcov,"# Age");                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
           }
   for(i=1; i<=nlstate;i++)          
     for(j=1; j<=(nlstate+ndeath);j++){          for(jk=-1; jk <=nlstate+ndeath; jk++)
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);            for(m=-1; m <=nlstate+ndeath; m++)
       fprintf(ficresprobcov," p%1d-%1d ",i,j);              if(freq[jk][m][i] !=0 ) {
       fprintf(ficresprobcor," p%1d-%1d ",i,j);              if(first==1)
     }                  printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   fprintf(ficresprob,"\n");                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   fprintf(ficresprobcov,"\n");              }
   fprintf(ficresprobcor,"\n");          if(i <= iagemax)
   xp=vector(1,npar);            fprintf(ficresp,"\n");
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);          if(first==1)
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));            printf("Others in log...\n");
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);          fprintf(ficlog,"\n");
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);        }
   first=1;      }
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    }
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    dateintmean=dateintsum/k2cpt; 
     exit(0);   
   }    fclose(ficresp);
   else{    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     fprintf(ficgp,"\n# Routine varprob");    free_vector(pp,1,nlstate);
   }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {    /* End of Freq */
     printf("Problem with html file: %s\n", optionfilehtm);  }
     exit(0);  
   }  /************ Prevalence ********************/
   else{  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)
     fprintf(fichtm,"\n<H2> Computing matrix of variance-covariance of step probabilities</h2>\n");  {  
     fprintf(fichtm,"\n<br> We 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");    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     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");       in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
   }    */
   cov[1]=1;   
   j=cptcoveff;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    double ***freq; /* Frequencies */
   j1=0;    double *pp, **prop;
   for(k1=1; k1<=1;k1++){    double pos,posprop; 
     for(i1=1; i1<=ncodemax[k1];i1++){    double  y2; /* in fractional years */
     j1++;    int iagemin, iagemax;
   
     if  (cptcovn>0) {    iagemin= (int) agemin;
       fprintf(ficresprob, "\n#********** Variable ");    iagemax= (int) agemax;
       fprintf(ficresprobcov, "\n#********** Variable ");    /*pp=vector(1,nlstate);*/
       fprintf(ficgp, "\n#********** Variable ");    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       fprintf(fichtm, "\n<h4>********** Variable</h4>\n ");    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       fprintf(ficresprobcor, "\n#********** Variable ");    j1=0;
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    
       fprintf(ficresprob, "**********\n#");    j=cptcoveff;
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       fprintf(ficresprobcov, "**********\n#");    
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    for(k1=1; k1<=j;k1++){
       fprintf(ficgp, "**********\n#");      for(i1=1; i1<=ncodemax[k1];i1++){
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        j1++;
       fprintf(ficgp, "**********\n#");        
       for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        for (i=1; i<=nlstate; i++)  
       fprintf(fichtm, "**********\n#");          for(m=iagemin; m <= iagemax+3; m++)
     }            prop[i][m]=0.0;
           
       for (age=bage; age<=fage; age ++){        for (i=1; i<=imx; i++) { /* Each individual */
         cov[2]=age;          bool=1;
         for (k=1; k<=cptcovn;k++) {          if  (cptcovn>0) {
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];            for (z1=1; z1<=cptcoveff; z1++) 
         }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];                bool=0;
         for (k=1; k<=cptcovprod;k++)          } 
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          if (bool==1) { 
                    for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         gp=vector(1,(nlstate)*(nlstate+ndeath));                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         gm=vector(1,(nlstate)*(nlstate+ndeath));                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                    if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
         for(theta=1; theta <=npar; theta++){                if (s[m][i]>0 && s[m][i]<=nlstate) { 
           for(i=1; i<=npar; i++)                  /*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]]);*/
             xp[i] = x[i] + (i==theta ?delti[theta]:0);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                            prop[s[m][i]][iagemax+3] += weight[i]; 
           pmij(pmmij,cov,ncovmodel,xp,nlstate);                } 
                        }
           k=0;            } /* end selection of waves */
           for(i=1; i<= (nlstate); i++){          }
             for(j=1; j<=(nlstate+ndeath);j++){        }
               k=k+1;        for(i=iagemin; i <= iagemax+3; i++){  
               gp[k]=pmmij[i][j];          
             }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
           }            posprop += prop[jk][i]; 
                    } 
           for(i=1; i<=npar; i++)  
             xp[i] = x[i] - (i==theta ?delti[theta]:0);          for(jk=1; jk <=nlstate ; jk++){     
                if( i <=  iagemax){ 
           pmij(pmmij,cov,ncovmodel,xp,nlstate);              if(posprop>=1.e-5){ 
           k=0;                probs[i][jk][j1]= prop[jk][i]/posprop;
           for(i=1; i<=(nlstate); i++){              } 
             for(j=1; j<=(nlstate+ndeath);j++){            } 
               k=k+1;          }/* end jk */ 
               gm[k]=pmmij[i][j];        }/* end i */ 
             }      } /* end i1 */
           }    } /* end k1 */
          
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      /*free_vector(pp,1,nlstate);*/
         }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)  
           for(theta=1; theta <=npar; theta++)  /************* Waves Concatenation ***************/
             trgradg[j][theta]=gradg[theta][j];  
          void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);  {
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
               Death is a valid wave (if date is known).
         pmij(pmmij,cov,ncovmodel,x,nlstate);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
               dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         k=0;       and mw[mi+1][i]. dh depends on stepm.
         for(i=1; i<=(nlstate); i++){       */
           for(j=1; j<=(nlstate+ndeath);j++){  
             k=k+1;    int i, mi, m;
             mu[k][(int) age]=pmmij[i][j];    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           }       double sum=0., jmean=0.;*/
         }    int first;
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)    int j, k=0,jk, ju, jl;
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)    double sum=0.;
             varpij[i][j][(int)age] = doldm[i][j];    first=0;
     jmin=1e+5;
         /*printf("\n%d ",(int)age);    jmax=-1;
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    jmean=0.;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    for(i=1; i<=imx; i++){
      }*/      mi=0;
       m=firstpass;
         fprintf(ficresprob,"\n%d ",(int)age);      while(s[m][i] <= nlstate){
         fprintf(ficresprobcov,"\n%d ",(int)age);        if(s[m][i]>=1)
         fprintf(ficresprobcor,"\n%d ",(int)age);          mw[++mi][i]=m;
         if(m >=lastpass)
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)          break;
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));        else
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){          m++;
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);      }/* end while */
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);      if (s[m][i] > nlstate){
         }        mi++;     /* Death is another wave */
         i=0;        /* if(mi==0)  never been interviewed correctly before death */
         for (k=1; k<=(nlstate);k++){           /* Only death is a correct wave */
           for (l=1; l<=(nlstate+ndeath);l++){        mw[mi][i]=m;
             i=i++;      }
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);  
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);      wav[i]=mi;
             for (j=1; j<=i;j++){      if(mi==0){
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);        nbwarn++;
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));        if(first==0){
             }          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           }          first=1;
         }/* end of loop for state */        }
       } /* end of loop for age */        if(first==1){
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
       for (k1=1; k1<=(nlstate);k1++){        }
         for (l1=1; l1<=(nlstate+ndeath);l1++){      } /* end mi==0 */
           if(l1==k1) continue;    } /* End individuals */
           i=(k1-1)*(nlstate+ndeath)+l1;  
           for (k2=1; k2<=(nlstate);k2++){    for(i=1; i<=imx; i++){
             for (l2=1; l2<=(nlstate+ndeath);l2++){      for(mi=1; mi<wav[i];mi++){
               if(l2==k2) continue;        if (stepm <=0)
               j=(k2-1)*(nlstate+ndeath)+l2;          dh[mi][i]=1;
               if(j<=i) continue;        else{
               for (age=bage; age<=fage; age ++){          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                 if ((int)age %5==0){            if (agedc[i] < 2*AGESUP) {
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;              if(j==0) j=1;  /* Survives at least one month after exam */
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;              else if(j<0){
                   mu1=mu[i][(int) age]/stepm*YEARM ;                nberr++;
                   mu2=mu[j][(int) age]/stepm*YEARM;                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]);
                   /* Computing eigen value of matrix of covariance */                j=1; /* Temporary Dangerous patch */
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));                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);
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                   printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);                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);
                   /* Eigen vectors */              }
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));              k=k+1;
                   v21=sqrt(1.-v11*v11);              if (j >= jmax) jmax=j;
                   v12=-v21;              if (j <= jmin) jmin=j;
                   v22=v11;              sum=sum+j;
                   /*printf(fignu*/              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */            }
                   if(first==1){          }
                     first=0;          else{
                     fprintf(ficgp,"\nset parametric;set nolabel");            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
                     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("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");            k=k+1;
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%1d%1d-%1d%1d.png\">varpijgr%s%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1);            if (j >= jmax) jmax=j;
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%1d%1d-%1d%1d.png\">, ",optionfilefiname,k2,l2,k1,l1);            else if (j <= jmin)jmin=j;
                     fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\"",optionfilefiname,k2,l2,k1,l1);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);            /*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]);*/
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);            if(j<0){
                     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\"",\              nberr++;
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \              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]);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);              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]);
                   }else{            }
                     first=0;            sum=sum+j;
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);          }
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);          jk= j/stepm;
                     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\"",\          jl= j -jk*stepm;
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \          ju= j -(jk+1)*stepm;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
                   }/* if first */            if(jl==0){
                 } /* age mod 5 */              dh[mi][i]=jk;
               } /* end loop age */              bh[mi][i]=0;
               fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\";replot;",optionfilefiname,k2,l2,k1,l1);            }else{ /* We want a negative bias in order to only have interpolation ie
               first=1;                    * at the price of an extra matrix product in likelihood */
             } /*l12 */              dh[mi][i]=jk+1;
           } /* k12 */              bh[mi][i]=ju;
         } /*l1 */            }
       }/* k1 */          }else{
     } /* loop covariates */            if(jl <= -ju){
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);              dh[mi][i]=jk;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));              bh[mi][i]=jl;       /* bias is positive if real duration
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));                                   * is higher than the multiple of stepm and negative otherwise.
     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);            else{
   }              dh[mi][i]=jk+1;
   free_vector(xp,1,npar);              bh[mi][i]=ju;
   fclose(ficresprob);            }
   fclose(ficresprobcov);            if(dh[mi][i]==0){
   fclose(ficresprobcor);              dh[mi][i]=1; /* At least one step */
   fclose(ficgp);              bh[mi][i]=ju; /* At least one step */
   fclose(fichtm);              /*  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);*/
 }            }
           } /* end if mle */
         }
 /******************* Printing html file ***********/      } /* end wave */
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    }
                   int lastpass, int stepm, int weightopt, char model[],\    jmean=sum/k;
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
                   int popforecast, int estepm ,\    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
                   double jprev1, double mprev1,double anprev1, \   }
                   double jprev2, double mprev2,double anprev2){  
   int jj1, k1, i1, cpt;  /*********** Tricode ****************************/
   /*char optionfilehtm[FILENAMELENGTH];*/  void tricode(int *Tvar, int **nbcode, int imx)
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {  {
     printf("Problem with %s \n",optionfilehtm), exit(0);    
   }    int Ndum[20],ij=1, k, j, i, maxncov=19;
     int cptcode=0;
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n    cptcoveff=0; 
  - 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    for (k=0; k<maxncov; k++) Ndum[k]=0;
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n    for (k=1; k<=7; k++) ncodemax[k]=0;
  - Life expectancies by age and initial health status (estepm=%2d months):  
    <a href=\"e%s\">e%s</a> <br>\n</li>", \    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n        Ndum[ij]++; /*store the modality */
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n                                         Tvar[j]. If V=sex and male is 0 and 
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n                                         female is 1, then  cptcode=1.*/
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n      }
  - 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);  
       for (i=0; i<=cptcode; i++) {
  if(popforecast==1) fprintf(fichtm,"\n        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 */
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n      }
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n  
         <br>",fileres,fileres,fileres,fileres);      ij=1; 
  else      for (i=1; i<=ncodemax[j]; i++) {
    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);        for (k=0; k<= maxncov; k++) {
 fprintf(fichtm," <li>Graphs</li><p>");          if (Ndum[k] != 0) {
             nbcode[Tvar[j]][ij]=k; 
  m=cptcoveff;            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}            
             ij++;
  jj1=0;          }
  for(k1=1; k1<=m;k1++){          if (ij > ncodemax[j]) break; 
    for(i1=1; i1<=ncodemax[k1];i1++){        }  
      jj1++;      } 
      if (cptcovn > 0) {    }  
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  
        for (cpt=1; cpt<=cptcoveff;cpt++)   for (k=0; k< maxncov; k++) Ndum[k]=0;
          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<=ncovmodel-2; i++) { 
      }     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
      /* Pij */     ij=Tvar[i];
      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>     Ndum[ij]++;
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);       }
      /* Quasi-incidences */  
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>   ij=1;
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);   for (i=1; i<= maxncov; i++) {
        /* Stable prevalence in each health state */     if((Ndum[i]!=0) && (i<=ncovcol)){
        for(cpt=1; cpt<nlstate;cpt++){       Tvaraff[ij]=i; /*For printing */
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>       ij++;
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);     }
        }   }
     for(cpt=1; cpt<=nlstate;cpt++) {   
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident   cptcoveff=ij-1; /*Number of simple covariates*/
 interval) in state (%d): v%s%d%d.png <br>  }
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    
      }  /*********** Health Expectancies ****************/
      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>  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 )
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
      }  {
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    /* Health expectancies */
 health expectancies in states (1) and (2): e%s%d.png<br>    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    double age, agelim, hf;
    }    double ***p3mat,***varhe;
  }    double **dnewm,**doldm;
 fclose(fichtm);    double *xp;
 }    double **gp, **gm;
     double ***gradg, ***trgradg;
 /******************* Gnuplot file **************/    int theta;
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    xp=vector(1,npar);
   int ng;    dnewm=matrix(1,nlstate*nlstate,1,npar);
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     printf("Problem with file %s",optionfilegnuplot);    
   }    fprintf(ficreseij,"# Health expectancies\n");
     fprintf(ficreseij,"# Age");
 #ifdef windows    for(i=1; i<=nlstate;i++)
     fprintf(ficgp,"cd \"%s\" \n",pathc);      for(j=1; j<=nlstate;j++)
 #endif        fprintf(ficreseij," %1d-%1d (SE)",i,j);
 m=pow(2,cptcoveff);    fprintf(ficreseij,"\n");
    
  /* 1eme*/    if(estepm < stepm){
   for (cpt=1; cpt<= nlstate ; cpt ++) {      printf ("Problem %d lower than %d\n",estepm, stepm);
    for (k1=1; k1<= m ; k1 ++) {    }
     else  hstepm=estepm;   
 #ifdef windows    /* We compute the life expectancy from trapezoids spaced every estepm months
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);     * This is mainly to measure the difference between two models: for example
      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);     * if stepm=24 months pijx are given only every 2 years and by summing them
 #endif     * we are calculating an estimate of the Life Expectancy assuming a linear 
 #ifdef unix     * progression in between and thus overestimating or underestimating according
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);     * to the curvature of the survival function. If, for the same date, we 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
 #endif     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
 for (i=1; i<= nlstate ; i ++) {     * curvature will be obtained if estepm is as small as stepm. */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /* For example we decided to compute the life expectancy with the smallest unit */
 }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);       nhstepm is the number of hstepm from age to agelim 
     for (i=1; i<= nlstate ; i ++) {       nstepm is the number of stepm from age to agelin. 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");       Look at hpijx to understand the reason of that which relies in memory size
   else fprintf(ficgp," \%%*lf (\%%*lf)");       and note for a fixed period like estepm months */
 }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);       survival function given by stepm (the optimization length). Unfortunately it
      for (i=1; i<= nlstate ; i ++) {       means that if the survival funtion is printed only each two years of age and if
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   else fprintf(ficgp," \%%*lf (\%%*lf)");       results. So we changed our mind and took the option of the best precision.
 }      */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 #ifdef unix  
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");    agelim=AGESUP;
 #endif    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
    }      /* nhstepm age range expressed in number of stepm */
   }      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   /*2 eme*/      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
   for (k1=1; k1<= m ; k1 ++) {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
          gp=matrix(0,nhstepm,1,nlstate*nlstate);
     for (i=1; i<= nlstate+1 ; i ++) {      gm=matrix(0,nhstepm,1,nlstate*nlstate);
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
       for (j=1; j<= nlstate+1 ; j ++) {         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   else fprintf(ficgp," \%%*lf (\%%*lf)");   
 }    
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      /* Computing  Variances of health expectancies */
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");       for(theta=1; theta <=npar; theta++){
         else fprintf(ficgp," \%%*lf (\%%*lf)");        for(i=1; i<=npar; i++){ 
 }            xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fprintf(ficgp,"\" t\"\" w l 0,");        }
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       for (j=1; j<= nlstate+1 ; j ++) {    
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        cptj=0;
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=1; j<= nlstate; j++){
 }            for(i=1; i<=nlstate; i++){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");            cptj=cptj+1;
       else fprintf(ficgp,"\" t\"\" w l 0,");            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
     }              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   }            }
            }
   /*3eme*/        }
        
   for (k1=1; k1<= m ; k1 ++) {       
     for (cpt=1; cpt<= nlstate ; cpt ++) {        for(i=1; i<=npar; i++) 
       k=2+nlstate*(2*cpt-2);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       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);        cptj=0;
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        for(j=1; j<= nlstate; j++){
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          for(i=1;i<=nlstate;i++){
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);            cptj=cptj+1;
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  
               gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
 */            }
       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);        }
         for(j=1; j<= nlstate*nlstate; j++)
       }          for(h=0; h<=nhstepm-1; h++){
     }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   }          }
         } 
   /* CV preval stat */     
     for (k1=1; k1<= m ; k1 ++) {  /* End theta */
     for (cpt=1; cpt<nlstate ; cpt ++) {  
       k=3;       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
       for (i=1; i< nlstate ; i ++)          for(theta=1; theta <=npar; theta++)
         fprintf(ficgp,"+$%d",k+i+1);            trgradg[h][j][theta]=gradg[h][theta][j];
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);       
        
       l=3+(nlstate+ndeath)*cpt;       for(i=1;i<=nlstate*nlstate;i++)
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        for(j=1;j<=nlstate*nlstate;j++)
       for (i=1; i< nlstate ; i ++) {          varhe[i][j][(int)age] =0.;
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);       printf("%d|",(int)age);fflush(stdout);
       }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);         for(h=0;h<=nhstepm-1;h++){
     }        for(k=0;k<=nhstepm-1;k++){
   }            matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   /* proba elementaires */          for(i=1;i<=nlstate*nlstate;i++)
    for(i=1,jk=1; i <=nlstate; i++){            for(j=1;j<=nlstate*nlstate;j++)
     for(k=1; k <=(nlstate+ndeath); k++){              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       if (k != i) {        }
         for(j=1; j <=ncovmodel; j++){      }
              /* Computing expectancies */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      for(i=1; i<=nlstate;i++)
           jk++;        for(j=1; j<=nlstate;j++)
           fprintf(ficgp,"\n");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
         }            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       }            
     }  /* 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]);*/
    }  
           }
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/  
      for(jk=1; jk <=m; jk++) {      fprintf(ficreseij,"%3.0f",age );
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);      cptj=0;
        if (ng==2)      for(i=1; i<=nlstate;i++)
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");        for(j=1; j<=nlstate;j++){
        else          cptj++;
          fprintf(ficgp,"\nset title \"Probability\"\n");          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);        }
        i=1;      fprintf(ficreseij,"\n");
        for(k2=1; k2<=nlstate; k2++) {     
          k3=i;      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
          for(k=1; k<=(nlstate+ndeath); k++) {      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
            if (k != k2){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
              if(ng==2)      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              else    }
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    printf("\n");
              ij=1;    fprintf(ficlog,"\n");
              for(j=3; j <=ncovmodel; j++) {  
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    free_vector(xp,1,npar);
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
                  ij++;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
                }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
                else  }
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
              }  /************ Variance ******************/
              fprintf(ficgp,")/(1");  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
                {
              for(k1=1; k1 <=nlstate; k1++){      /* Variance of health expectancies */
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
                ij=1;    /* double **newm;*/
                for(j=3; j <=ncovmodel; j++){    double **dnewm,**doldm;
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double **dnewmp,**doldmp;
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    int i, j, nhstepm, hstepm, h, nstepm ;
                    ij++;    int k, cptcode;
                  }    double *xp;
                  else    double **gp, **gm;  /* for var eij */
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    double ***gradg, ***trgradg; /*for var eij */
                }    double **gradgp, **trgradgp; /* for var p point j */
                fprintf(ficgp,")");    double *gpp, *gmp; /* for var p point j */
              }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);    double ***p3mat;
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    double age,agelim, hf;
              i=i+ncovmodel;    double ***mobaverage;
            }    int theta;
          }    char digit[4];
        }    char digitp[25];
      }  
    }    char fileresprobmorprev[FILENAMELENGTH];
    fclose(ficgp);  
 }  /* end gnuplot */    if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
 /*************** Moving average **************/      else strcpy(digitp,"-populbased-nomobil-");
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    }
     else 
   int i, cpt, cptcod;      strcpy(digitp,"-stablbased-");
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)  
       for (i=1; i<=nlstate;i++)    if (mobilav!=0) {
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           mobaverage[(int)agedeb][i][cptcod]=0.;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
            fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       for (i=1; i<=nlstate;i++){      }
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    }
           for (cpt=0;cpt<=4;cpt++){  
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    strcpy(fileresprobmorprev,"prmorprev"); 
           }    sprintf(digit,"%-d",ij);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
         }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     }    strcat(fileresprobmorprev,fileres);
        if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
 }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
 /************** Forecasting ******************/    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 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){    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   int *popage;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      fprintf(ficresprobmorprev," p.%-d SE",j);
   double *popeffectif,*popcount;      for(i=1; i<=nlstate;i++)
   double ***p3mat;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   char fileresf[FILENAMELENGTH];    }  
     fprintf(ficresprobmorprev,"\n");
  agelim=AGESUP;    fprintf(ficgp,"\n# Routine varevsij");
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    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);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  /*   } */
      varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    
   strcpy(fileresf,"f");    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");
   strcat(fileresf,fileres);    fprintf(ficresvij,"# Age");
   if((ficresf=fopen(fileresf,"w"))==NULL) {    for(i=1; i<=nlstate;i++)
     printf("Problem with forecast resultfile: %s\n", fileresf);      for(j=1; j<=nlstate;j++)
   }        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   printf("Computing forecasting: result on file '%s' \n", fileresf);    fprintf(ficresvij,"\n");
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
   if (mobilav==1) {    doldm=matrix(1,nlstate,1,nlstate);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     movingaverage(agedeb, fage, ageminpar, mobaverage);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }  
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    gpp=vector(nlstate+1,nlstate+ndeath);
   if (stepm<=12) stepsize=1;    gmp=vector(nlstate+1,nlstate+ndeath);
      trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   agelim=AGESUP;    
      if(estepm < stepm){
   hstepm=1;      printf ("Problem %d lower than %d\n",estepm, stepm);
   hstepm=hstepm/stepm;    }
   yp1=modf(dateintmean,&yp);    else  hstepm=estepm;   
   anprojmean=yp;    /* For example we decided to compute the life expectancy with the smallest unit */
   yp2=modf((yp1*12),&yp);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   mprojmean=yp;       nhstepm is the number of hstepm from age to agelim 
   yp1=modf((yp2*30.5),&yp);       nstepm is the number of stepm from age to agelin. 
   jprojmean=yp;       Look at hpijx to understand the reason of that which relies in memory size
   if(jprojmean==0) jprojmean=1;       and note for a fixed period like k years */
   if(mprojmean==0) jprojmean=1;    /* 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
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);       means that if the survival funtion is printed every two years of age and if
         you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   for(cptcov=1;cptcov<=i2;cptcov++){       results. So we changed our mind and took the option of the best precision.
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    */
       k=k+1;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       fprintf(ficresf,"\n#******");    agelim = AGESUP;
       for(j=1;j<=cptcoveff;j++) {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       fprintf(ficresf,"******\n");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficresf,"# StartingAge FinalAge");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      gp=matrix(0,nhstepm,1,nlstate);
            gm=matrix(0,nhstepm,1,nlstate);
        
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {  
         fprintf(ficresf,"\n");      for(theta=1; theta <=npar; theta++){
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);          for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           nhstepm = nhstepm/hstepm;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if (popbased==1) {
           oldm=oldms;savm=savms;          if(mobilav ==0){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for(i=1; i<=nlstate;i++)
                      prlim[i][i]=probs[(int)age][i][ij];
           for (h=0; h<=nhstepm; h++){          }else{ /* mobilav */ 
             if (h==(int) (calagedate+YEARM*cpt)) {            for(i=1; i<=nlstate;i++)
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);              prlim[i][i]=mobaverage[(int)age][i][ij];
             }          }
             for(j=1; j<=nlstate+ndeath;j++) {        }
               kk1=0.;kk2=0;    
               for(i=1; i<=nlstate;i++) {                      for(j=1; j<= nlstate; j++){
                 if (mobilav==1)          for(h=0; h<=nhstepm; h++){
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                 else {              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          }
                 }        }
                        /* This for computing probability of death (h=1 means
               }           computed over hstepm matrices product = hstepm*stepm months) 
               if (h==(int)(calagedate+12*cpt)){           as a weighted average of prlim.
                 fprintf(ficresf," %.3f", kk1);        */
                                for(j=nlstate+1;j<=nlstate+ndeath;j++){
               }          for(i=1,gpp[j]=0.; i<= nlstate; i++)
             }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
           }        }    
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        /* end probability of death */
         }  
       }        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
         if (popbased==1) {
   fclose(ficresf);          if(mobilav ==0){
 }            for(i=1; i<=nlstate;i++)
 /************** Forecasting ******************/              prlim[i][i]=probs[(int)age][i][ij];
 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){          }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;              prlim[i][i]=mobaverage[(int)age][i][ij];
   int *popage;          }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        }
   double *popeffectif,*popcount;  
   double ***p3mat,***tabpop,***tabpopprev;        for(j=1; j<= nlstate; j++){
   char filerespop[FILENAMELENGTH];          for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
   agelim=AGESUP;        }
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;        /* This for computing probability of death (h=1 means
             computed over hstepm matrices product = hstepm*stepm months) 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);           as a weighted average of prlim.
          */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
   strcpy(filerespop,"pop");          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   strcat(filerespop,fileres);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        }    
     printf("Problem with forecast resultfile: %s\n", filerespop);        /* end probability of death */
   }  
   printf("Computing forecasting: result on file '%s' \n", filerespop);        for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     movingaverage(agedeb, fage, ageminpar, mobaverage);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   }        }
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;      } /* End theta */
   if (stepm<=12) stepsize=1;  
        trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   agelim=AGESUP;  
        for(h=0; h<=nhstepm; h++) /* veij */
   hstepm=1;        for(j=1; j<=nlstate;j++)
   hstepm=hstepm/stepm;          for(theta=1; theta <=npar; theta++)
              trgradg[h][j][theta]=gradg[h][theta][j];
   if (popforecast==1) {  
     if((ficpop=fopen(popfile,"r"))==NULL) {      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       printf("Problem with population file : %s\n",popfile);exit(0);        for(theta=1; theta <=npar; theta++)
     }          trgradgp[j][theta]=gradgp[theta][j];
     popage=ivector(0,AGESUP);    
     popeffectif=vector(0,AGESUP);  
     popcount=vector(0,AGESUP);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
          for(i=1;i<=nlstate;i++)
     i=1;          for(j=1;j<=nlstate;j++)
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;          vareij[i][j][(int)age] =0.;
      
     imx=i;      for(h=0;h<=nhstepm;h++){
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        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(cptcov=1;cptcov<=i2;cptcov++){          for(i=1;i<=nlstate;i++)
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            for(j=1;j<=nlstate;j++)
       k=k+1;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       fprintf(ficrespop,"\n#******");        }
       for(j=1;j<=cptcoveff;j++) {      }
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       }      /* pptj */
       fprintf(ficrespop,"******\n");      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       fprintf(ficrespop,"# Age");      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
       if (popforecast==1)  fprintf(ficrespop," [Population]");        for(i=nlstate+1;i<=nlstate+ndeath;i++)
                varppt[j][i]=doldmp[j][i];
       for (cpt=0; cpt<=0;cpt++) {      /* end ppptj */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        /*  x centered again */
              hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);   
           nhstepm = nhstepm/hstepm;      if (popbased==1) {
                  if(mobilav ==0){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(i=1; i<=nlstate;i++)
           oldm=oldms;savm=savms;            prlim[i][i]=probs[(int)age][i][ij];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          }else{ /* mobilav */ 
                  for(i=1; i<=nlstate;i++)
           for (h=0; h<=nhstepm; h++){            prlim[i][i]=mobaverage[(int)age][i][ij];
             if (h==(int) (calagedate+YEARM*cpt)) {        }
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      }
             }               
             for(j=1; j<=nlstate+ndeath;j++) {      /* This for computing probability of death (h=1 means
               kk1=0.;kk2=0;         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
               for(i=1; i<=nlstate;i++) {                       as a weighted average of prlim.
                 if (mobilav==1)      */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      for(j=nlstate+1;j<=nlstate+ndeath;j++){
                 else {        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
                 }      }    
               }      /* end probability of death */
               if (h==(int)(calagedate+12*cpt)){  
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
                   /*fprintf(ficrespop," %.3f", kk1);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
               }        for(i=1; i<=nlstate;i++){
             }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
             for(i=1; i<=nlstate;i++){        }
               kk1=0.;      } 
                 for(j=1; j<=nlstate;j++){      fprintf(ficresprobmorprev,"\n");
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  
                 }      fprintf(ficresvij,"%.0f ",age );
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      for(i=1; i<=nlstate;i++)
             }        for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        }
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      fprintf(ficresvij,"\n");
           }      free_matrix(gp,0,nhstepm,1,nlstate);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      free_matrix(gm,0,nhstepm,1,nlstate);
         }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       }      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /******/    } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    free_vector(gmp,nlstate+1,nlstate+ndeath);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
           nhstepm = nhstepm/hstepm;    /* 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)\";");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
           oldm=oldms;savm=savms;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
           for (h=0; h<=nhstepm; h++){    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
             if (h==(int) (calagedate+YEARM*cpt)) {    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
             }    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
             for(j=1; j<=nlstate+ndeath;j++) {    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);
               kk1=0.;kk2=0;    /*  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);
               for(i=1; i<=nlstate;i++) {                */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
               }    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  
             }    free_vector(xp,1,npar);
           }    free_matrix(doldm,1,nlstate,1,nlstate);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_matrix(dnewm,1,nlstate,1,npar);
         }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       }    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
    }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      fclose(ficresprobmorprev);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fflush(ficgp);
     fflush(fichtm); 
   if (popforecast==1) {  }  /* end varevsij */
     free_ivector(popage,0,AGESUP);  
     free_vector(popeffectif,0,AGESUP);  /************ Variance of prevlim ******************/
     free_vector(popcount,0,AGESUP);  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)
   }  {
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /* Variance of prevalence limit */
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   fclose(ficrespop);    double **newm;
 }    double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
 /***********************************************/    int k, cptcode;
 /**************** Main Program *****************/    double *xp;
 /***********************************************/    double *gp, *gm;
     double **gradg, **trgradg;
 int main(int argc, char *argv[])    double age,agelim;
 {    int theta;
      
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   double agedeb, agefin,hf;    fprintf(ficresvpl,"# Age");
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
   double fret;    fprintf(ficresvpl,"\n");
   double **xi,tmp,delta;  
     xp=vector(1,npar);
   double dum; /* Dummy variable */    dnewm=matrix(1,nlstate,1,npar);
   double ***p3mat;    doldm=matrix(1,nlstate,1,nlstate);
   int *indx;    
   char line[MAXLINE], linepar[MAXLINE];    hstepm=1*YEARM; /* Every year of age */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   int firstobs=1, lastobs=10;    agelim = AGESUP;
   int sdeb, sfin; /* Status at beginning and end */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   int c,  h , cpt,l;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   int ju,jl, mi;      if (stepm >= YEARM) hstepm=1;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      gradg=matrix(1,npar,1,nlstate);
   int mobilav=0,popforecast=0;      gp=vector(1,nlstate);
   int hstepm, nhstepm;      gm=vector(1,nlstate);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;  
       for(theta=1; theta <=npar; theta++){
   double bage, fage, age, agelim, agebase;        for(i=1; i<=npar; i++){ /* Computes gradient */
   double ftolpl=FTOL;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   double **prlim;        }
   double *severity;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   double ***param; /* Matrix of parameters */        for(i=1;i<=nlstate;i++)
   double  *p;          gp[i] = prlim[i][i];
   double **matcov; /* Matrix of covariance */      
   double ***delti3; /* Scale */        for(i=1; i<=npar; i++) /* Computes gradient */
   double *delti; /* Scale */          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   double ***eij, ***vareij;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   double **varpl; /* Variances of prevalence limits by age */        for(i=1;i<=nlstate;i++)
   double *epj, vepp;          gm[i] = prlim[i][i];
   double kk1, kk2;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;        for(i=1;i<=nlstate;i++)
            gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
       trgradg =matrix(1,nlstate,1,npar);
   
   char z[1]="c", occ;      for(j=1; j<=nlstate;j++)
 #include <sys/time.h>        for(theta=1; theta <=npar; theta++)
 #include <time.h>          trgradg[j][theta]=gradg[theta][j];
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  
        for(i=1;i<=nlstate;i++)
   /* long total_usecs;        varpl[i][(int)age] =0.;
   struct timeval start_time, end_time;      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
        matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      for(i=1;i<=nlstate;i++)
   getcwd(pathcd, size);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
   printf("\n%s",version);      fprintf(ficresvpl,"%.0f ",age );
   if(argc <=1){      for(i=1; i<=nlstate;i++)
     printf("\nEnter the parameter file name: ");        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
     scanf("%s",pathtot);      fprintf(ficresvpl,"\n");
   }      free_vector(gp,1,nlstate);
   else{      free_vector(gm,1,nlstate);
     strcpy(pathtot,argv[1]);      free_matrix(gradg,1,npar,1,nlstate);
   }      free_matrix(trgradg,1,nlstate,1,npar);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    } /* End age */
   /*cygwin_split_path(pathtot,path,optionfile);  
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    free_vector(xp,1,npar);
   /* cutv(path,optionfile,pathtot,'\\');*/    free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  }
   chdir(path);  
   replace(pathc,path);  /************ 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)
 /*-------- arguments in the command line --------*/  {
     int i, j=0,  i1, k1, l1, t, tj;
   strcpy(fileres,"r");    int k2, l2, j1,  z1;
   strcat(fileres, optionfilefiname);    int k=0,l, cptcode;
   strcat(fileres,".txt");    /* Other files have txt extension */    int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   /*---------arguments file --------*/    double **dnewm,**doldm;
     double *xp;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    double *gp, *gm;
     printf("Problem with optionfile %s\n",optionfile);    double **gradg, **trgradg;
     goto end;    double **mu;
   }    double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   strcpy(filereso,"o");    int theta;
   strcat(filereso,fileres);    char fileresprob[FILENAMELENGTH];
   if((ficparo=fopen(filereso,"w"))==NULL) {    char fileresprobcov[FILENAMELENGTH];
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    char fileresprobcor[FILENAMELENGTH];
   }  
     double ***varpij;
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    strcpy(fileresprob,"prob"); 
     ungetc(c,ficpar);    strcat(fileresprob,fileres);
     fgets(line, MAXLINE, ficpar);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     puts(line);      printf("Problem with resultfile: %s\n", fileresprob);
     fputs(line,ficparo);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   }    }
   ungetc(c,ficpar);    strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
   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((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   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);      printf("Problem with resultfile: %s\n", fileresprobcov);
   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,"Problem with resultfile: %s\n", fileresprobcov);
 while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    strcpy(fileresprobcor,"probcor"); 
     fgets(line, MAXLINE, ficpar);    strcat(fileresprobcor,fileres);
     puts(line);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     fputs(line,ficparo);      printf("Problem with resultfile: %s\n", fileresprobcor);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   ungetc(c,ficpar);    }
      printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
        fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   covar=matrix(0,NCOVMAX,1,n);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   cptcovn=0;    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   ncovmodel=2+cptcovn;    
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
      fprintf(ficresprob,"# Age");
   /* Read guess parameters */    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   /* Reads comments: lines beginning with '#' */    fprintf(ficresprobcov,"# Age");
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     ungetc(c,ficpar);    fprintf(ficresprobcov,"# Age");
     fgets(line, MAXLINE, ficpar);  
     puts(line);  
     fputs(line,ficparo);    for(i=1; i<=nlstate;i++)
   }      for(j=1; j<=(nlstate+ndeath);j++){
   ungetc(c,ficpar);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
          fprintf(ficresprobcov," p%1d-%1d ",i,j);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     for(i=1; i <=nlstate; i++)      }  
     for(j=1; j <=nlstate+ndeath-1; j++){   /* fprintf(ficresprob,"\n");
       fscanf(ficpar,"%1d%1d",&i1,&j1);    fprintf(ficresprobcov,"\n");
       fprintf(ficparo,"%1d%1d",i1,j1);    fprintf(ficresprobcor,"\n");
       printf("%1d%1d",i,j);   */
       for(k=1; k<=ncovmodel;k++){   xp=vector(1,npar);
         fscanf(ficpar," %lf",&param[i][j][k]);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         printf(" %lf",param[i][j][k]);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
         fprintf(ficparo," %lf",param[i][j][k]);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       }    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
       fscanf(ficpar,"\n");    first=1;
       printf("\n");    fprintf(ficgp,"\n# Routine varprob");
       fprintf(ficparo,"\n");    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     }    fprintf(fichtm,"\n");
    
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
   p=param[1][1];    file %s<br>\n",optionfilehtmcov);
      fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   /* Reads comments: lines beginning with '#' */  and drawn. It helps understanding how is the covariance between two incidences.\
   while((c=getc(ficpar))=='#' && c!= EOF){   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     ungetc(c,ficpar);    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. \
     fgets(line, MAXLINE, ficpar);  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
     puts(line);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
     fputs(line,ficparo);  standard deviations wide on each axis. <br>\
   }   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
   ungetc(c,ficpar);   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    cov[1]=1;
   for(i=1; i <=nlstate; i++){    tj=cptcoveff;
     for(j=1; j <=nlstate+ndeath-1; j++){    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
       fscanf(ficpar,"%1d%1d",&i1,&j1);    j1=0;
       printf("%1d%1d",i,j);    for(t=1; t<=tj;t++){
       fprintf(ficparo,"%1d%1d",i1,j1);      for(i1=1; i1<=ncodemax[t];i1++){ 
       for(k=1; k<=ncovmodel;k++){        j1++;
         fscanf(ficpar,"%le",&delti3[i][j][k]);        if  (cptcovn>0) {
         printf(" %le",delti3[i][j][k]);          fprintf(ficresprob, "\n#********** Variable "); 
         fprintf(ficparo," %le",delti3[i][j][k]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(ficresprob, "**********\n#\n");
       fscanf(ficpar,"\n");          fprintf(ficresprobcov, "\n#********** Variable "); 
       printf("\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fprintf(ficparo,"\n");          fprintf(ficresprobcov, "**********\n#\n");
     }          
   }          fprintf(ficgp, "\n#********** Variable "); 
   delti=delti3[1][1];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficgp, "**********\n#\n");
   /* Reads comments: lines beginning with '#' */          
   while((c=getc(ficpar))=='#' && c!= EOF){          
     ungetc(c,ficpar);          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     fgets(line, MAXLINE, ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     puts(line);          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     fputs(line,ficparo);          
   }          fprintf(ficresprobcor, "\n#********** Variable ");    
   ungetc(c,ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresprobcor, "**********\n#");    
   matcov=matrix(1,npar,1,npar);        }
   for(i=1; i <=npar; i++){        
     fscanf(ficpar,"%s",&str);        for (age=bage; age<=fage; age ++){ 
     printf("%s",str);          cov[2]=age;
     fprintf(ficparo,"%s",str);          for (k=1; k<=cptcovn;k++) {
     for(j=1; j <=i; j++){            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
       fscanf(ficpar," %le",&matcov[i][j]);          }
       printf(" %.5le",matcov[i][j]);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       fprintf(ficparo," %.5le",matcov[i][j]);          for (k=1; k<=cptcovprod;k++)
     }            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     fscanf(ficpar,"\n");          
     printf("\n");          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     fprintf(ficparo,"\n");          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   }          gp=vector(1,(nlstate)*(nlstate+ndeath));
   for(i=1; i <=npar; i++)          gm=vector(1,(nlstate)*(nlstate+ndeath));
     for(j=i+1;j<=npar;j++)      
       matcov[i][j]=matcov[j][i];          for(theta=1; theta <=npar; theta++){
                for(i=1; i<=npar; i++)
   printf("\n");              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
     /*-------- Rewriting paramater file ----------*/            
      strcpy(rfileres,"r");    /* "Rparameterfile */            k=0;
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/            for(i=1; i<= (nlstate); i++){
      strcat(rfileres,".");    /* */              for(j=1; j<=(nlstate+ndeath);j++){
      strcat(rfileres,optionfilext);    /* Other files have txt extension */                k=k+1;
     if((ficres =fopen(rfileres,"w"))==NULL) {                gp[k]=pmmij[i][j];
       printf("Problem writing new parameter file: %s\n", fileres);goto end;              }
     }            }
     fprintf(ficres,"#%s\n",version);            
                for(i=1; i<=npar; i++)
     /*-------- data file ----------*/              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     if((fic=fopen(datafile,"r"))==NULL)    {      
       printf("Problem with datafile: %s\n", datafile);goto end;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     }            k=0;
             for(i=1; i<=(nlstate); i++){
     n= lastobs;              for(j=1; j<=(nlstate+ndeath);j++){
     severity = vector(1,maxwav);                k=k+1;
     outcome=imatrix(1,maxwav+1,1,n);                gm[k]=pmmij[i][j];
     num=ivector(1,n);              }
     moisnais=vector(1,n);            }
     annais=vector(1,n);       
     moisdc=vector(1,n);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     andc=vector(1,n);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     agedc=vector(1,n);          }
     cod=ivector(1,n);  
     weight=vector(1,n);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */            for(theta=1; theta <=npar; theta++)
     mint=matrix(1,maxwav,1,n);              trgradg[j][theta]=gradg[theta][j];
     anint=matrix(1,maxwav,1,n);          
     s=imatrix(1,maxwav+1,1,n);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     adl=imatrix(1,maxwav+1,1,n);              matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     tab=ivector(1,NCOVMAX);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     ncodemax=ivector(1,8);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     i=1;          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     while (fgets(line, MAXLINE, fic) != NULL)    {  
       if ((i >= firstobs) && (i <=lastobs)) {          pmij(pmmij,cov,ncovmodel,x,nlstate);
                  
         for (j=maxwav;j>=1;j--){          k=0;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          for(i=1; i<=(nlstate); i++){
           strcpy(line,stra);            for(j=1; j<=(nlstate+ndeath);j++){
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              k=k+1;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              mu[k][(int) age]=pmmij[i][j];
         }            }
                  }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
         for (j=ncovcol;j>=1;j--){            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);            }*/
         }  
         num[i]=atol(stra);          fprintf(ficresprob,"\n%d ",(int)age);
                  fprintf(ficresprobcov,"\n%d ",(int)age);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          fprintf(ficresprobcor,"\n%d ",(int)age);
           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;}*/  
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
         i=i+1;            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     }            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     /* printf("ii=%d", ij);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
        scanf("%d",i);*/          }
   imx=i-1; /* Number of individuals */          i=0;
           for (k=1; k<=(nlstate);k++){
   /* for (i=1; i<=imx; i++){            for (l=1; l<=(nlstate+ndeath);l++){ 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;              i=i++;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     }*/              for (j=1; j<=i;j++){
    /*  for (i=1; i<=imx; i++){                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
      if (s[4][i]==9)  s[4][i]=-1;                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
      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]));}*/              }
              }
            }/* end of loop for state */
   /* Calculation of the number of parameter from char model*/        } /* end of loop for age */
   Tvar=ivector(1,15);  
   Tprod=ivector(1,15);        /* Confidence intervalle of pij  */
   Tvaraff=ivector(1,15);        /*
   Tvard=imatrix(1,15,1,2);          fprintf(ficgp,"\nset noparametric;unset label");
   Tage=ivector(1,15);                fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
              fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   if (strlen(model) >1){          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);
     j=0, j1=0, k1=1, k2=1;          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     j=nbocc(model,'+');          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     j1=nbocc(model,'*');          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     cptcovn=j+1;        */
     cptcovprod=j1;  
            /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     strcpy(modelsav,model);        first1=1;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        for (k2=1; k2<=(nlstate);k2++){
       printf("Error. Non available option model=%s ",model);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
       goto end;            if(l2==k2) continue;
     }            j=(k2-1)*(nlstate+ndeath)+l2;
                for (k1=1; k1<=(nlstate);k1++){
     for(i=(j+1); i>=1;i--){              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
       cutv(stra,strb,modelsav,'+');                if(l1==k1) continue;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);                i=(k1-1)*(nlstate+ndeath)+l1;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                if(i<=j) continue;
       /*scanf("%d",i);*/                for (age=bage; age<=fage; age ++){ 
       if (strchr(strb,'*')) {                  if ((int)age %5==0){
         cutv(strd,strc,strb,'*');                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
         if (strcmp(strc,"age")==0) {                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
           cptcovprod--;                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
           cutv(strb,stre,strd,'V');                    mu1=mu[i][(int) age]/stepm*YEARM ;
           Tvar[i]=atoi(stre);                    mu2=mu[j][(int) age]/stepm*YEARM;
           cptcovage++;                    c12=cv12/sqrt(v1*v2);
             Tage[cptcovage]=i;                    /* Computing eigen value of matrix of covariance */
             /*printf("stre=%s ", stre);*/                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         }                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         else if (strcmp(strd,"age")==0) {                    /* Eigen vectors */
           cptcovprod--;                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
           cutv(strb,stre,strc,'V');                    /*v21=sqrt(1.-v11*v11); *//* error */
           Tvar[i]=atoi(stre);                    v21=(lc1-v1)/cv12*v11;
           cptcovage++;                    v12=-v21;
           Tage[cptcovage]=i;                    v22=v11;
         }                    tnalp=v21/v11;
         else {                    if(first1==1){
           cutv(strb,stre,strc,'V');                      first1=0;
           Tvar[i]=ncovcol+k1;                      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);
           cutv(strb,strc,strd,'V');                    }
           Tprod[k1]=i;                    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);
           Tvard[k1][1]=atoi(strc);                    /*printf(fignu*/
           Tvard[k1][2]=atoi(stre);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
           Tvar[cptcovn+k2]=Tvard[k1][1];                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                    if(first==1){
           for (k=1; k<=lastobs;k++)                      first=0;
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                      fprintf(ficgp,"\nset parametric;unset label");
           k1++;                      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);
           k2=k2+2;                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
         }                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
       }   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
       else {  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
        /*  scanf("%d",i);*/                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
       cutv(strd,strc,strb,'V');                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
       Tvar[i]=atoi(strc);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
       }                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
       strcpy(modelsav,stra);                        fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
         scanf("%d",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)) not",\
     }                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
 }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                      }else{
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                      first=0;
   printf("cptcovprod=%d ", cptcovprod);                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
   scanf("%d ",i);*/                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     fclose(fic);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
     /*  if(mle==1){*/                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     if (weightopt != 1) { /* Maximisation without weights*/                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       for(i=1;i<=n;i++) weight[i]=1.0;                    }/* if first */
     }                  } /* age mod 5 */
     /*-calculation of age at interview from date of interview and age at death -*/                } /* end loop age */
     agev=matrix(1,maxwav,1,imx);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
     for (i=1; i<=imx; i++) {              } /*l12 */
       for(m=2; (m<= maxwav); m++) {            } /* k12 */
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          } /*l1 */
          anint[m][i]=9999;        }/* k1 */
          s[m][i]=-1;      } /* loop covariates */
        }    }
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
       }    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     }    free_vector(xp,1,npar);
     fclose(ficresprob);
     for (i=1; i<=imx; i++)  {    fclose(ficresprobcov);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    fclose(ficresprobcor);
       for(m=1; (m<= maxwav); m++){    fflush(ficgp);
         if(s[m][i] >0){    fflush(fichtmcov);
           if (s[m][i] >= nlstate+1) {  }
             if(agedc[i]>0)  
               if(moisdc[i]!=99 && andc[i]!=9999)  
                 agev[m][i]=agedc[i];  /******************* Printing html file ***********/
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
            else {                    int lastpass, int stepm, int weightopt, char model[],\
               if (andc[i]!=9999){                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                    int popforecast, int estepm ,\
               agev[m][i]=-1;                    double jprev1, double mprev1,double anprev1, \
               }                    double jprev2, double mprev2,double anprev2){
             }    int jj1, k1, i1, cpt;
           }  
           else if(s[m][i] !=9){ /* Should no more exist */     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
             if(mint[m][i]==99 || anint[m][i]==9999)             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
               agev[m][i]=1;     fprintf(fichtm,"\
             else if(agev[m][i] <agemin){   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
               agemin=agev[m][i];             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/     fprintf(fichtm,"\
             }   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
             else if(agev[m][i] >agemax){             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
               agemax=agev[m][i];     fprintf(fichtm,"\
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/   - Life expectancies by age and initial health status (estepm=%2d months): \
             }     <a href=\"%s\">%s</a> <br>\n</li>",
             /*agev[m][i]=anint[m][i]-annais[i];*/             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
             /*   agev[m][i] = age[i]+2*m;*/  
           }  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
           else { /* =9 */  
             agev[m][i]=1;   m=cptcoveff;
             s[m][i]=-1;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
           }  
         }   jj1=0;
         else /*= 0 Unknown */   for(k1=1; k1<=m;k1++){
           agev[m][i]=1;     for(i1=1; i1<=ncodemax[k1];i1++){
       }       jj1++;
           if (cptcovn > 0) {
     }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     for (i=1; i<=imx; i++)  {         for (cpt=1; cpt<=cptcoveff;cpt++) 
       for(m=1; (m<= maxwav); m++){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
         if (s[m][i] > (nlstate+ndeath)) {         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           printf("Error: Wrong value in nlstate or ndeath\n");         }
           goto end;       /* Pij */
         }       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
       }  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
     }       /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
     free_vector(severity,1,maxwav);         /* Stable prevalence in each health state */
     free_imatrix(outcome,1,maxwav+1,1,n);         for(cpt=1; cpt<nlstate;cpt++){
     free_vector(moisnais,1,n);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
     free_vector(annais,1,n);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
     /* free_matrix(mint,1,maxwav,1,n);         }
        free_matrix(anint,1,maxwav,1,n);*/       for(cpt=1; cpt<=nlstate;cpt++) {
     free_vector(moisdc,1,n);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
     free_vector(andc,1,n);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
         } /* end i1 */
     wav=ivector(1,imx);   }/* End k1 */
     dh=imatrix(1,lastpass-firstpass+1,1,imx);   fprintf(fichtm,"</ul>");
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  
      
     /* Concatenates waves */   fprintf(fichtm,"\
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  \n<br><li><h4> Result files (second order: variances)</h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
       Tcode=ivector(1,100);   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
       ncodemax[1]=1;   fprintf(fichtm,"\
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
                 subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
    codtab=imatrix(1,100,1,10);  
    h=0;   fprintf(fichtm,"\
    m=pow(2,cptcoveff);   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
             subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    for(k=1;k<=cptcoveff; k++){   fprintf(fichtm,"\
      for(i=1; i <=(m/pow(2,k));i++){   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
        for(j=1; j <= ncodemax[k]; j++){           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){   fprintf(fichtm,"\
            h++;   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/   fprintf(fichtm,"\
          }   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
        }           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
      }  
    }  /*  if(popforecast==1) fprintf(fichtm,"\n */
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
       codtab[1][2]=1;codtab[2][2]=2; */  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
    /* for(i=1; i <=m ;i++){  /*      <br>",fileres,fileres,fileres,fileres); */
       for(k=1; k <=cptcovn; k++){  /*  else  */
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
       }   fflush(fichtm);
       printf("\n");   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
       }  
       scanf("%d",i);*/   m=cptcoveff;
       if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    /* Calculates basic frequencies. Computes observed prevalence at single age  
        and prints on file fileres'p'. */   jj1=0;
    for(k1=1; k1<=m;k1++){
         for(i1=1; i1<=ncodemax[k1];i1++){
           jj1++;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       if (cptcovn > 0) {
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         for (cpt=1; cpt<=cptcoveff;cpt++) 
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
             }
     /* For Powell, parameters are in a vector p[] starting at p[1]       for(cpt=1; cpt<=nlstate;cpt++) {
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
     if(mle==1){       }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);       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);
     /*--------- results files --------------*/     } /* end i1 */
     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);   }/* End k1 */
     fprintf(fichtm,"</ul>");
    fflush(fichtm);
    jk=1;  }
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  /******************* Gnuplot file **************/
    for(i=1,jk=1; i <=nlstate; i++){  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
      for(k=1; k <=(nlstate+ndeath); k++){  
        if (k != i)    char dirfileres[132],optfileres[132];
          {    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
            printf("%d%d ",i,k);    int ng;
            fprintf(ficres,"%1d%1d ",i,k);  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
            for(j=1; j <=ncovmodel; j++){  /*     printf("Problem with file %s",optionfilegnuplot); */
              printf("%f ",p[jk]);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
              fprintf(ficres,"%f ",p[jk]);  /*   } */
              jk++;  
            }    /*#ifdef windows */
            printf("\n");    fprintf(ficgp,"cd \"%s\" \n",pathc);
            fprintf(ficres,"\n");      /*#endif */
          }    m=pow(2,cptcoveff);
      }  
    }    strcpy(dirfileres,optionfilefiname);
  if(mle==1){    strcpy(optfileres,"vpl");
     /* Computing hessian and covariance matrix */   /* 1eme*/
     ftolhess=ftol; /* Usually correct */    for (cpt=1; cpt<= nlstate ; cpt ++) {
     hesscov(matcov, p, npar, delti, ftolhess, func);     for (k1=1; k1<= m ; k1 ++) {
  }       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
     printf("# Scales (for hessian or gradient estimation)\n");       fprintf(ficgp,"set xlabel \"Age\" \n\
      for(i=1,jk=1; i <=nlstate; i++){  set ylabel \"Probability\" \n\
       for(j=1; j <=nlstate+ndeath; j++){  set ter png small\n\
         if (j!=i) {  set size 0.65,0.65\n\
           fprintf(ficres,"%1d%1d",i,j);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
           printf("%1d%1d",i,j);  
           for(k=1; k<=ncovmodel;k++){       for (i=1; i<= nlstate ; i ++) {
             printf(" %.5e",delti[jk]);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
             fprintf(ficres," %.5e",delti[jk]);         else fprintf(ficgp," \%%*lf (\%%*lf)");
             jk++;       }
           }       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);
           printf("\n");       for (i=1; i<= nlstate ; i ++) {
           fprintf(ficres,"\n");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         }         else fprintf(ficgp," \%%*lf (\%%*lf)");
       }       } 
      }       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
           for (i=1; i<= nlstate ; i ++) {
     k=1;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");         else fprintf(ficgp," \%%*lf (\%%*lf)");
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");       }  
     for(i=1;i<=npar;i++){       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
       /*  if (k>nlstate) k=1;     }
       i1=(i-1)/(ncovmodel*nlstate)+1;    }
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    /*2 eme*/
       printf("%s%d%d",alph[k],i1,tab[i]);*/    
       fprintf(ficres,"%3d",i);    for (k1=1; k1<= m ; k1 ++) { 
       printf("%3d",i);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       for(j=1; j<=i;j++){      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
         fprintf(ficres," %.5e",matcov[i][j]);      
         printf(" %.5e",matcov[i][j]);      for (i=1; i<= nlstate+1 ; i ++) {
       }        k=2*i;
       fprintf(ficres,"\n");        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       printf("\n");        for (j=1; j<= nlstate+1 ; j ++) {
       k++;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     }          else fprintf(ficgp," \%%*lf (\%%*lf)");
            }   
     while((c=getc(ficpar))=='#' && c!= EOF){        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
       ungetc(c,ficpar);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
       fgets(line, MAXLINE, ficpar);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       puts(line);        for (j=1; j<= nlstate+1 ; j ++) {
       fputs(line,ficparo);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     }          else fprintf(ficgp," \%%*lf (\%%*lf)");
     ungetc(c,ficpar);        }   
     estepm=0;        fprintf(ficgp,"\" t\"\" w l 0,");
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     if (estepm==0 || estepm < stepm) estepm=stepm;        for (j=1; j<= nlstate+1 ; j ++) {
     if (fage <= 2) {          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       bage = ageminpar;          else fprintf(ficgp," \%%*lf (\%%*lf)");
       fage = agemaxpar;        }   
     }        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
            else fprintf(ficgp,"\" t\"\" w l 0,");
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      }
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    }
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    
      /*3eme*/
     while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);    for (k1=1; k1<= m ; k1 ++) { 
     fgets(line, MAXLINE, ficpar);      for (cpt=1; cpt<= nlstate ; cpt ++) {
     puts(line);        k=2+nlstate*(2*cpt-2);
     fputs(line,ficparo);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
   }        fprintf(ficgp,"set ter png small\n\
   ungetc(c,ficpar);  set size 0.65,0.65\n\
    plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   while((c=getc(ficpar))=='#' && c!= EOF){          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     ungetc(c,ficpar);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     fgets(line, MAXLINE, ficpar);          
     puts(line);        */
     fputs(line,ficparo);        for (i=1; i< nlstate ; i ++) {
   }          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
   ungetc(c,ficpar);          
          } 
       }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    }
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    
     /* CV preval stable (period) */
   fscanf(ficpar,"pop_based=%d\n",&popbased);    for (k1=1; k1<= m ; k1 ++) { 
   fprintf(ficparo,"pop_based=%d\n",popbased);        for (cpt=1; cpt<=nlstate ; cpt ++) {
   fprintf(ficres,"pop_based=%d\n",popbased);          k=3;
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
   while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
     ungetc(c,ficpar);  set ter png small\nset size 0.65,0.65\n\
     fgets(line, MAXLINE, ficpar);  unset log y\n\
     puts(line);  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
     fputs(line,ficparo);        
   }        for (i=1; i< nlstate ; i ++)
   ungetc(c,ficpar);          fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   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);        
 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);        l=3+(nlstate+ndeath)*cpt;
 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);        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
 while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficgp,"+$%d",l+i+1);
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
     puts(line);      } 
     fputs(line,ficparo);    }  
   }    
   ungetc(c,ficpar);    /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);      for(k=1; k <=(nlstate+ndeath); k++){
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        if (k != i) {
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            jk++; 
             fprintf(ficgp,"\n");
 /*------------ gnuplot -------------*/          }
   strcpy(optionfilegnuplot,optionfilefiname);        }
   strcat(optionfilegnuplot,".gp");      }
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {     }
     printf("Problem with file %s",optionfilegnuplot);  
   }     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   fclose(ficgp);       for(jk=1; jk <=m; jk++) {
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
 /*--------- index.htm --------*/         if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   strcpy(optionfilehtm,optionfile);         else
   strcat(optionfilehtm,".htm");           fprintf(ficgp,"\nset title \"Probability\"\n");
   if((fichtm=fopen(optionfilehtm,"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 %s \n",optionfilehtm), exit(0);         i=1;
   }         for(k2=1; k2<=nlstate; k2++) {
            k3=i;
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n           for(k=1; k<=(nlstate+ndeath); k++) {
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n             if (k != k2){
 \n               if(ng==2)
 Total number of observations=%d <br>\n                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n               else
 <hr  size=\"2\" color=\"#EC5E5E\">                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
  <ul><li>Parameter files<br>\n               ij=1;
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n               for(j=3; j <=ncovmodel; j++) {
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   fclose(fichtm);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);                 }
                   else
 /*------------ free_vector  -------------*/                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
  chdir(path);               }
                 fprintf(ficgp,")/(1");
  free_ivector(wav,1,imx);               
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);               for(k1=1; k1 <=nlstate; k1++){   
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                   fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
  free_ivector(num,1,n);                 ij=1;
  free_vector(agedc,1,n);                 for(j=3; j <=ncovmodel; j++){
  /*free_matrix(covar,1,NCOVMAX,1,n);*/                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
  fclose(ficparo);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
  fclose(ficres);                     ij++;
                    }
                    else
   /*--------------- Prevalence limit --------------*/                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                   }
   strcpy(filerespl,"pl");                 fprintf(ficgp,")");
   strcat(filerespl,fileres);               }
   if((ficrespl=fopen(filerespl,"w"))==NULL) {               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   }               i=i+ncovmodel;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);             }
   fprintf(ficrespl,"#Prevalence limit\n");           } /* end k */
   fprintf(ficrespl,"#Age ");         } /* end k2 */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);       } /* end jk */
   fprintf(ficrespl,"\n");     } /* end ng */
       fflush(ficgp); 
   prlim=matrix(1,nlstate,1,nlstate);  }  /* end gnuplot */
   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 */  /*************** Moving average **************/
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;    int i, cpt, cptcod;
   agebase=ageminpar;    int modcovmax =1;
   agelim=agemaxpar;    int mobilavrange, mob;
   ftolpl=1.e-10;    double age;
   i1=cptcoveff;  
   if (cptcovn < 1){i1=1;}    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
   for(cptcov=1;cptcov<=i1;cptcov++){    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
         k=k+1;    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      if(mobilav==1) mobilavrange=5; /* default */
         fprintf(ficrespl,"\n#******");      else mobilavrange=mobilav;
         for(j=1;j<=cptcoveff;j++)      for (age=bage; age<=fage; age++)
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for (i=1; i<=nlstate;i++)
         fprintf(ficrespl,"******\n");          for (cptcod=1;cptcod<=modcovmax;cptcod++)
                    mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
         for (age=agebase; age<=agelim; age++){      /* We keep the original values on the extreme ages bage, fage and for 
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
           fprintf(ficrespl,"%.0f",age );         we use a 5 terms etc. until the borders are no more concerned. 
           for(i=1; i<=nlstate;i++)      */ 
           fprintf(ficrespl," %.5f", prlim[i][i]);      for (mob=3;mob <=mobilavrange;mob=mob+2){
           fprintf(ficrespl,"\n");        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
         }          for (i=1; i<=nlstate;i++){
       }            for (cptcod=1;cptcod<=modcovmax;cptcod++){
     }              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   fclose(ficrespl);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
   /*------------- h Pij x at various ages ------------*/                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                  }
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {            }
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          }
   }        }/* end age */
   printf("Computing pij: result on file '%s' \n", filerespij);      }/* end mob */
      }else return -1;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    return 0;
   /*if (stepm<=24) stepsize=2;*/  }/* End movingaverage */
   
   agelim=AGESUP;  
   hstepm=stepsize*YEARM; /* Every year of age */  /************** Forecasting ******************/
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
      /* proj1, year, month, day of starting projection 
   k=0;       agemin, agemax range of age
   for(cptcov=1;cptcov<=i1;cptcov++){       dateprev1 dateprev2 range of dates during which prevalence is computed
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       anproj2 year of en of projection (same day and month as proj1).
       k=k+1;    */
         fprintf(ficrespij,"\n#****** ");    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
         for(j=1;j<=cptcoveff;j++)    int *popage;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double agec; /* generic age */
         fprintf(ficrespij,"******\n");    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
            double *popeffectif,*popcount;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    double ***p3mat;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double ***mobaverage;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    char fileresf[FILENAMELENGTH];
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;    agelim=AGESUP;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
           fprintf(ficrespij,"# Age");   
           for(i=1; i<=nlstate;i++)    strcpy(fileresf,"f"); 
             for(j=1; j<=nlstate+ndeath;j++)    strcat(fileresf,fileres);
               fprintf(ficrespij," %1d-%1d",i,j);    if((ficresf=fopen(fileresf,"w"))==NULL) {
           fprintf(ficrespij,"\n");      printf("Problem with forecast resultfile: %s\n", fileresf);
            for (h=0; h<=nhstepm; h++){      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    }
             for(i=1; i<=nlstate;i++)    printf("Computing forecasting: result on file '%s' \n", fileresf);
               for(j=1; j<=nlstate+ndeath;j++)    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
             fprintf(ficrespij,"\n");    if (cptcoveff==0) ncodemax[cptcoveff]=1;
              }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if (mobilav!=0) {
           fprintf(ficrespij,"\n");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         }      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    }
   
   fclose(ficrespij);    stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
   /*---------- Forecasting ------------------*/      printf ("Problem %d lower than %d\n",estepm, stepm);
   if((stepm == 1) && (strcmp(model,".")==0)){    }
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    else  hstepm=estepm;   
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  
   }    hstepm=hstepm/stepm; 
   else{    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
     erreur=108;                                 fractional in yp1 */
     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);    anprojmean=yp;
   }    yp2=modf((yp1*12),&yp);
      mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
   /*---------- Health expectancies and variances ------------*/    jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
   strcpy(filerest,"t");    if(mprojmean==0) jprojmean=1;
   strcat(filerest,fileres);  
   if((ficrest=fopen(filerest,"w"))==NULL) {    i1=cptcoveff;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    if (cptcovn < 1){i1=1;}
   }    
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   strcpy(filerese,"e");  
   strcat(filerese,fileres);  /*            if (h==(int)(YEARM*yearp)){ */
   if((ficreseij=fopen(filerese,"w"))==NULL) {    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   }        k=k+1;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
  strcpy(fileresv,"v");          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]]);
   strcat(fileresv,fileres);        }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        fprintf(ficresf,"******\n");
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
   }        for(j=1; j<=nlstate+ndeath;j++){ 
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          for(i=1; i<=nlstate;i++)              
   calagedate=-1;            fprintf(ficresf," p%d%d",i,j);
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          fprintf(ficresf," p.%d",j);
         }
   k=0;        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(ficresf,"\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
       k=k+1;  
       fprintf(ficrest,"\n#****** ");          for (agec=fage; agec>=(ageminpar-1); agec--){ 
       for(j=1;j<=cptcoveff;j++)            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            nhstepm = nhstepm/hstepm; 
       fprintf(ficrest,"******\n");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
       fprintf(ficreseij,"\n#****** ");            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
       for(j=1;j<=cptcoveff;j++)          
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for (h=0; h<=nhstepm; h++){
       fprintf(ficreseij,"******\n");              if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
       fprintf(ficresvij,"\n#****** ");                for(j=1;j<=cptcoveff;j++) 
       for(j=1;j<=cptcoveff;j++)                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
       fprintf(ficresvij,"******\n");              } 
               for(j=1; j<=nlstate+ndeath;j++) {
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                ppij=0.;
       oldm=oldms;savm=savms;                for(i=1; i<=nlstate;i++) {
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);                    if (mobilav==1) 
                      ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                  else {
       oldm=oldms;savm=savms;                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);                  }
                      if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                    }
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                } /* end i */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                if (h*hstepm/YEARM*stepm==yearp) {
       fprintf(ficrest,"\n");                  fprintf(ficresf," %.3f", ppij);
                 }
       epj=vector(1,nlstate+1);              }/* end j */
       for(age=bage; age <=fage ;age++){            } /* end h */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         if (popbased==1) {          } /* end agec */
           for(i=1; i<=nlstate;i++)        } /* end yearp */
             prlim[i][i]=probs[(int)age][i][k];      } /* end cptcod */
         }    } /* end  cptcov */
                 
         fprintf(ficrest," %4.0f",age);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    fclose(ficresf);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];  }
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/  
           }  /************** Forecasting *****not tested NB*************/
           epj[nlstate+1] +=epj[j];  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;
         for(i=1, vepp=0.;i <=nlstate;i++)    int *popage;
           for(j=1;j <=nlstate;j++)    double calagedatem, agelim, kk1, kk2;
             vepp += vareij[i][j][(int)age];    double *popeffectif,*popcount;
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    double ***p3mat,***tabpop,***tabpopprev;
         for(j=1;j <=nlstate;j++){    double ***mobaverage;
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    char filerespop[FILENAMELENGTH];
         }  
         fprintf(ficrest,"\n");    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       }    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }    agelim=AGESUP;
   }    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
 free_matrix(mint,1,maxwav,1,n);    
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     free_vector(weight,1,n);    
   fclose(ficreseij);    
   fclose(ficresvij);    strcpy(filerespop,"pop"); 
   fclose(ficrest);    strcat(filerespop,fileres);
   fclose(ficpar);    if((ficrespop=fopen(filerespop,"w"))==NULL) {
   free_vector(epj,1,nlstate+1);      printf("Problem with forecast resultfile: %s\n", filerespop);
        fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
   /*------- Variance limit prevalence------*/      }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
   strcpy(fileresvpl,"vpl");    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   strcat(fileresvpl,fileres);  
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    if (cptcoveff==0) ncodemax[cptcoveff]=1;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  
     exit(0);    if (mobilav!=0) {
   }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   k=0;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   for(cptcov=1;cptcov<=i1;cptcov++){      }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    }
       k=k+1;  
       fprintf(ficresvpl,"\n#****** ");    stepsize=(int) (stepm+YEARM-1)/YEARM;
       for(j=1;j<=cptcoveff;j++)    if (stepm<=12) stepsize=1;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       fprintf(ficresvpl,"******\n");    agelim=AGESUP;
          
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    hstepm=1;
       oldm=oldms;savm=savms;    hstepm=hstepm/stepm; 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    
     }    if (popforecast==1) {
  }      if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
   fclose(ficresvpl);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
   /*---------- End : free ----------------*/      popage=ivector(0,AGESUP);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      popeffectif=vector(0,AGESUP);
        popcount=vector(0,AGESUP);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      i=1;   
        while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
       
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      imx=i;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    }
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);  
      for(cptcov=1,k=0;cptcov<=i2;cptcov++){
   free_matrix(matcov,1,npar,1,npar);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   free_vector(delti,1,npar);        k=k+1;
   free_matrix(agev,1,maxwav,1,imx);        fprintf(ficrespop,"\n#******");
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   fprintf(fichtm,"\n</body>");        }
   fclose(fichtm);        fprintf(ficrespop,"******\n");
   fclose(ficgp);        fprintf(ficrespop,"# Age");
          for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
   if(erreur >0)        
     printf("End of Imach with error or warning %d\n",erreur);        for (cpt=0; cpt<=0;cpt++) { 
   else   printf("End of Imach\n");          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          
            for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   /*printf("Total time was %d uSec.\n", total_usecs);*/            nhstepm = nhstepm/hstepm; 
   /*------ End -----------*/            
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
  end:            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
 #ifdef windows          
   /* chdir(pathcd);*/            for (h=0; h<=nhstepm; h++){
 #endif              if (h==(int) (calagedatem+YEARM*cpt)) {
  /*system("wgnuplot graph.plt");*/                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
  /*system("../gp37mgw/wgnuplot graph.plt");*/              } 
  /*system("cd ../gp37mgw");*/              for(j=1; j<=nlstate+ndeath;j++) {
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/                kk1=0.;kk2=0;
  strcpy(plotcmd,GNUPLOTPROGRAM);                for(i=1; i<=nlstate;i++) {              
  strcat(plotcmd," ");                  if (mobilav==1) 
  strcat(plotcmd,optionfilegnuplot);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
  system(plotcmd);                  else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
 #ifdef windows                  }
   while (z[0] != 'q') {                }
     /* chdir(path); */                if (h==(int)(calagedatem+12*cpt)){
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
     scanf("%s",z);                    /*fprintf(ficrespop," %.3f", kk1);
     if (z[0] == 'c') system("./imach");                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
     else if (z[0] == 'e') system(optionfilehtm);                }
     else if (z[0] == 'g') system(plotcmd);              }
     else if (z[0] == 'q') exit(0);              for(i=1; i<=nlstate;i++){
   }                kk1=0.;
 #endif                  for(j=1; j<=nlstate;j++){
 }                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       sump=sump+1;
       num=num+1;
     }
    
    
     /* for (i=1; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=0;i<=imx-1 ; i++)
       {
         if (cens[i]==1 & wav[i]>1)
           A=-x[1]/(x[2])*
             (exp(x[2]/YEARM*(agecens[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)));
         
         if (cens[i]==0 & wav[i]>1)
           A=-x[1]/(x[2])*
                (exp(x[2]/YEARM*(agedc[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)))
             +log(x[1]/YEARM)+x[2]/YEARM*(agedc[i]*12-agegomp*12)+log(YEARM);      
         
         if (wav[i]>1 & agecens[i]>15) {
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov){
     int i;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (j=1; j<=lastpass; j++)
           if (s[j][i]>nlstate) {
             dcwave[i]=j;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];agecens[i]=1.; 
           if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
           cens[i]=1;
           
           if (ageexmed[i]<1) cens[i]=-1;
           if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
   
       p[1]=0.1; p[2]=0.1;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow-mort"); 
     strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
     /*  for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     */
     fprintf(ficrespow,"\n");
   
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM,delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov);
     } /* Endof if mle==-3 */
   
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
       fprintf(ficrespl,"#Stable prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
   
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /*---------- Health expectancies and variances ------------*/
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total LEs with variances: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficreseij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
           }
   
    
           fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficreseij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of stable prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
     strcpy(plotcmd,"\"");
     strcat(plotcmd,pathimach);
     strcat(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd,"\"");
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     if((outcmd=system(plotcmd)) != 0){
       printf(" Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.47  
changed lines
  Added in v.1.101


FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>