Diff for /imach/src/imach.c between versions 1.50 and 1.122

version 1.50, 2002/06/26 23:25:02 version 1.122, 2006/03/20 09:45:41
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.122  2006/03/20 09:45:41  brouard
      (Module): Weights can have a decimal point as for
   This program computes Healthy Life Expectancies from    English (a comma might work with a correct LC_NUMERIC environment,
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    otherwise the weight is truncated).
   first survey ("cross") where individuals from different ages are    Modification of warning when the covariates values are not 0 or
   interviewed on their health status or degree of disability (in the    1.
   case of a health survey which is our main interest) -2- at least a    Version 0.98g
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.121  2006/03/16 17:45:01  lievre
   computed from the time spent in each health state according to a    * imach.c (Module): Comments concerning covariates added
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    * imach.c (Module): refinements in the computation of lli if
   simplest model is the multinomial logistic model where pij is the    status=-2 in order to have more reliable computation if stepm is
   probability to be observed in state j at the second wave    not 1 month. Version 0.98f
   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    Revision 1.120  2006/03/16 15:10:38  lievre
   'age' is age and 'sex' is a covariate. If you want to have a more    (Module): refinements in the computation of lli if
   complex model than "constant and age", you should modify the program    status=-2 in order to have more reliable computation if stepm is
   where the markup *Covariates have to be included here again* invites    not 1 month. Version 0.98f
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.119  2006/03/15 17:42:26  brouard
     (Module): Bug if status = -2, the loglikelihood was
   The advantage of this computer programme, compared to a simple    computed as likelihood omitting the logarithm. Version O.98e
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.118  2006/03/14 18:20:07  brouard
   intermediate interview, the information is lost, but taken into    (Module): varevsij Comments added explaining the second
   account using an interpolation or extrapolation.      table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   hPijx is the probability to be observed in state i at age x+h    (Module): Function pstamp added
   conditional to the observed state i at age x. The delay 'h' can be    (Module): Version 0.98d
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    Revision 1.117  2006/03/14 17:16:22  brouard
   semester or year) is model as a multinomial logistic.  The hPx    (Module): varevsij Comments added explaining the second
   matrix is simply the matrix product of nh*stepm elementary matrices    table of variances if popbased=1 .
   and the contribution of each individual to the likelihood is simply    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   hPijx.    (Module): Function pstamp added
     (Module): Version 0.98d
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.116  2006/03/06 10:29:27  brouard
      (Module): Variance-covariance wrong links and
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    varian-covariance of ej. is needed (Saito).
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.115  2006/02/27 12:17:45  brouard
   from the European Union.    (Module): One freematrix added in mlikeli! 0.98c
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.114  2006/02/26 12:57:58  brouard
   can be accessed at http://euroreves.ined.fr/imach .    (Module): Some improvements in processing parameter
   **********************************************************************/    filename with strsep.
    
 #include <math.h>    Revision 1.113  2006/02/24 14:20:24  brouard
 #include <stdio.h>    (Module): Memory leaks checks with valgrind and:
 #include <stdlib.h>    datafile was not closed, some imatrix were not freed and on matrix
 #include <unistd.h>    allocation too.
   
 #define MAXLINE 256    Revision 1.112  2006/01/30 09:55:26  brouard
 #define GNUPLOTPROGRAM "gnuplot"    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Revision 1.111  2006/01/25 20:38:18  brouard
 /*#define DEBUG*/    (Module): Lots of cleaning and bugs added (Gompertz)
 #define windows    (Module): Comments can be added in data file. Missing date values
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    can be a simple dot '.'.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.110  2006/01/25 00:51:50  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    (Module): Lots of cleaning and bugs added (Gompertz)
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.109  2006/01/24 19:37:15  brouard
 #define NINTERVMAX 8    (Module): Comments (lines starting with a #) are allowed in data.
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.108  2006/01/19 18:05:42  lievre
 #define NCOVMAX 8 /* Maximum number of covariates */    Gnuplot problem appeared...
 #define MAXN 20000    To be fixed
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.107  2006/01/19 16:20:37  brouard
 #define AGEBASE 40    Test existence of gnuplot in imach path
 #ifdef windows  
 #define DIRSEPARATOR '\\'    Revision 1.106  2006/01/19 13:24:36  brouard
 #define ODIRSEPARATOR '/'    Some cleaning and links added in html output
 #else  
 #define DIRSEPARATOR '/'    Revision 1.105  2006/01/05 20:23:19  lievre
 #define ODIRSEPARATOR '\\'    *** empty log message ***
 #endif  
     Revision 1.104  2005/09/30 16:11:43  lievre
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    (Module): sump fixed, loop imx fixed, and simplifications.
 int erreur; /* Error number */    (Module): If the status is missing at the last wave but we know
 int nvar;    that the person is alive, then we can code his/her status as -2
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    (instead of missing=-1 in earlier versions) and his/her
 int npar=NPARMAX;    contributions to the likelihood is 1 - Prob of dying from last
 int nlstate=2; /* Number of live states */    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 int ndeath=1; /* Number of dead states */    the healthy state at last known wave). Version is 0.98
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.103  2005/09/30 15:54:49  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.102  2004/09/15 17:31:30  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    Add the possibility to read data file including tab characters.
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.101  2004/09/15 10:38:38  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Fix on curr_time
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.100  2004/07/12 18:29:06  brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Add version for Mac OS X. Just define UNIX in Makefile
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficlog;    Revision 1.99  2004/06/05 08:57:40  brouard
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    *** empty log message ***
 FILE *ficresprobmorprev;  
 FILE *fichtm; /* Html File */    Revision 1.98  2004/05/16 15:05:56  brouard
 FILE *ficreseij;    New version 0.97 . First attempt to estimate force of mortality
 char filerese[FILENAMELENGTH];    directly from the data i.e. without the need of knowing the health
 FILE  *ficresvij;    state at each age, but using a Gompertz model: log u =a + b*age .
 char fileresv[FILENAMELENGTH];    This is the basic analysis of mortality and should be done before any
 FILE  *ficresvpl;    other analysis, in order to test if the mortality estimated from the
 char fileresvpl[FILENAMELENGTH];    cross-longitudinal survey is different from the mortality estimated
 char title[MAXLINE];    from other sources like vital statistic data.
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    The same imach parameter file can be used but the option for mle should be -3.
   
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    Agnès, who wrote this part of the code, tried to keep most of the
 char filelog[FILENAMELENGTH]; /* Log file */    former routines in order to include the new code within the former code.
 char filerest[FILENAMELENGTH];  
 char fileregp[FILENAMELENGTH];    The output is very simple: only an estimate of the intercept and of
 char popfile[FILENAMELENGTH];    the slope with 95% confident intervals.
   
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    Current limitations:
     A) Even if you enter covariates, i.e. with the
 #define NR_END 1    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define FREE_ARG char*    B) There is no computation of Life Expectancy nor Life Table.
 #define FTOL 1.0e-10  
     Revision 1.97  2004/02/20 13:25:42  lievre
 #define NRANSI    Version 0.96d. Population forecasting command line is (temporarily)
 #define ITMAX 200    suppressed.
   
 #define TOL 2.0e-4    Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #define CGOLD 0.3819660    rewritten within the same printf. Workaround: many printfs.
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.95  2003/07/08 07:54:34  brouard
     * imach.c (Repository):
 #define GOLD 1.618034    (Repository): Using imachwizard code to output a more meaningful covariance
 #define GLIMIT 100.0    matrix (cov(a12,c31) instead of numbers.
 #define TINY 1.0e-20  
     Revision 1.94  2003/06/27 13:00:02  brouard
 static double maxarg1,maxarg2;    Just cleaning
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.93  2003/06/25 16:33:55  brouard
      (Module): On windows (cygwin) function asctime_r doesn't
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    exist so I changed back to asctime which exists.
 #define rint(a) floor(a+0.5)    (Module): Version 0.96b
   
 static double sqrarg;    Revision 1.92  2003/06/25 16:30:45  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    (Module): On windows (cygwin) function asctime_r doesn't
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    exist so I changed back to asctime which exists.
   
 int imx;    Revision 1.91  2003/06/25 15:30:29  brouard
 int stepm;    * imach.c (Repository): Duplicated warning errors corrected.
 /* Stepm, step in month: minimum step interpolation*/    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
 int estepm;    is stamped in powell.  We created a new html file for the graphs
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    concerning matrix of covariance. It has extension -cov.htm.
   
 int m,nb;    Revision 1.90  2003/06/24 12:34:15  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    (Module): Some bugs corrected for windows. Also, when
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    mle=-1 a template is output in file "or"mypar.txt with the design
 double **pmmij, ***probs, ***mobaverage;    of the covariance matrix to be input.
 double dateintmean=0;  
     Revision 1.89  2003/06/24 12:30:52  brouard
 double *weight;    (Module): Some bugs corrected for windows. Also, when
 int **s; /* Status */    mle=-1 a template is output in file "or"mypar.txt with the design
 double *agedc, **covar, idx;    of the covariance matrix to be input.
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.88  2003/06/23 17:54:56  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.87  2003/06/18 12:26:01  brouard
 /**************** split *************************/    Version 0.96
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Revision 1.86  2003/06/17 20:04:08  brouard
    char *s;                             /* pointer */    (Module): Change position of html and gnuplot routines and added
    int  l1, l2;                         /* length counters */    routine fileappend.
   
    l1 = strlen( path );                 /* length of path */    Revision 1.85  2003/06/17 13:12:43  brouard
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    * imach.c (Repository): Check when date of death was earlier that
    s= strrchr( path, DIRSEPARATOR );            /* find last / */    current date of interview. It may happen when the death was just
    if ( s == NULL ) {                   /* no directory, so use current */    prior to the death. In this case, dh was negative and likelihood
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)    was wrong (infinity). We still send an "Error" but patch by
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/    assuming that the date of death was just one stepm after the
 #if     defined(__bsd__)                /* get current working directory */    interview.
       extern char       *getwd( );    (Repository): Because some people have very long ID (first column)
     we changed int to long in num[] and we added a new lvector for
       if ( getwd( dirc ) == NULL ) {    memory allocation. But we also truncated to 8 characters (left
 #else    truncation)
       extern char       *getcwd( );    (Repository): No more line truncation errors.
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.84  2003/06/13 21:44:43  brouard
 #endif    * imach.c (Repository): Replace "freqsummary" at a correct
          return( GLOCK_ERROR_GETCWD );    place. It differs from routine "prevalence" which may be called
       }    many times. Probs is memory consuming and must be used with
       strcpy( name, path );             /* we've got it */    parcimony.
    } else {                             /* strip direcotry from path */    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    Revision 1.83  2003/06/10 13:39:11  lievre
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    *** empty log message ***
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Revision 1.82  2003/06/05 15:57:20  brouard
       dirc[l1-l2] = 0;                  /* add zero */    Add log in  imach.c and  fullversion number is now printed.
    }  
    l1 = strlen( dirc );                 /* length of directory */  */
 #ifdef windows  /*
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }     Interpolated Markov Chain
 #else  
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    Short summary of the programme:
 #endif    
    s = strrchr( name, '.' );            /* find last / */    This program computes Healthy Life Expectancies from
    s++;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
    strcpy(ext,s);                       /* save extension */    first survey ("cross") where individuals from different ages are
    l1= strlen( name);    interviewed on their health status or degree of disability (in the
    l2= strlen( s)+1;    case of a health survey which is our main interest) -2- at least a
    strncpy( finame, name, l1-l2);    second wave of interviews ("longitudinal") which measure each change
    finame[l1-l2]= 0;    (if any) in individual health status.  Health expectancies are
    return( 0 );                         /* we're done */    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
     Maximum Likelihood of the parameters involved in the model.  The
     simplest model is the multinomial logistic model where pij is the
 /******************************************/    probability to be observed in state j at the second wave
     conditional to be observed in state i at the first wave. Therefore
 void replace(char *s, char*t)    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 {    'age' is age and 'sex' is a covariate. If you want to have a more
   int i;    complex model than "constant and age", you should modify the program
   int lg=20;    where the markup *Covariates have to be included here again* invites
   i=0;    you to do it.  More covariates you add, slower the
   lg=strlen(t);    convergence.
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    The advantage of this computer programme, compared to a simple
     if (t[i]== '\\') s[i]='/';    multinomial logistic model, is clear when the delay between waves is not
   }    identical for each individual. Also, if a individual missed an
 }    intermediate interview, the information is lost, but taken into
     account using an interpolation or extrapolation.  
 int nbocc(char *s, char occ)  
 {    hPijx is the probability to be observed in state i at age x+h
   int i,j=0;    conditional to the observed state i at age x. The delay 'h' can be
   int lg=20;    split into an exact number (nh*stepm) of unobserved intermediate
   i=0;    states. This elementary transition (by month, quarter,
   lg=strlen(s);    semester or year) is modelled as a multinomial logistic.  The hPx
   for(i=0; i<= lg; i++) {    matrix is simply the matrix product of nh*stepm elementary matrices
   if  (s[i] == occ ) j++;    and the contribution of each individual to the likelihood is simply
   }    hPijx.
   return j;  
 }    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the period (stable) prevalence. 
 void cutv(char *u,char *v, char*t, char occ)    
 {    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   /* cuts string t into u and v where u is ended by char occ excluding it             Institut national d'études démographiques, Paris.
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)    This software have been partly granted by Euro-REVES, a concerted action
      gives u="abcedf" and v="ghi2j" */    from the European Union.
   int i,lg,j,p=0;    It is copyrighted identically to a GNU software product, ie programme and
   i=0;    software can be distributed freely for non commercial use. Latest version
   for(j=0; j<=strlen(t)-1; j++) {    can be accessed at http://euroreves.ined.fr/imach .
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   lg=strlen(t);    
   for(j=0; j<p; j++) {    **********************************************************************/
     (u[j] = t[j]);  /*
   }    main
      u[p]='\0';    read parameterfile
     read datafile
    for(j=0; j<= lg; j++) {    concatwav
     if (j>=(p+1))(v[j-p-1] = t[j]);    freqsummary
   }    if (mle >= 1)
 }      mlikeli
     print results files
 /********************** nrerror ********************/    if mle==1 
        computes hessian
 void nrerror(char error_text[])    read end of parameter file: agemin, agemax, bage, fage, estepm
 {        begin-prev-date,...
   fprintf(stderr,"ERREUR ...\n");    open gnuplot file
   fprintf(stderr,"%s\n",error_text);    open html file
   exit(1);    period (stable) prevalence
 }     for age prevalim()
 /*********************** vector *******************/    h Pij x
 double *vector(int nl, int nh)    variance of p varprob
 {    forecasting if prevfcast==1 prevforecast call prevalence()
   double *v;    health expectancies
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Variance-covariance of DFLE
   if (!v) nrerror("allocation failure in vector");    prevalence()
   return v-nl+NR_END;     movingaverage()
 }    varevsij() 
     if popbased==1 varevsij(,popbased)
 /************************ free vector ******************/    total life expectancies
 void free_vector(double*v, int nl, int nh)    Variance of period (stable) prevalence
 {   end
   free((FREE_ARG)(v+nl-NR_END));  */
 }  
   
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)   
 {  #include <math.h>
   int *v;  #include <stdio.h>
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #include <stdlib.h>
   if (!v) nrerror("allocation failure in ivector");  #include <string.h>
   return v-nl+NR_END;  #include <unistd.h>
 }  
   #include <limits.h>
 /******************free ivector **************************/  #include <sys/types.h>
 void free_ivector(int *v, long nl, long nh)  #include <sys/stat.h>
 {  #include <errno.h>
   free((FREE_ARG)(v+nl-NR_END));  extern int errno;
 }  
   /* #include <sys/time.h> */
 /******************* imatrix *******************************/  #include <time.h>
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #include "timeval.h"
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {  /* #include <libintl.h> */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  /* #define _(String) gettext (String) */
   int **m;  
    #define MAXLINE 256
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #define GNUPLOTPROGRAM "gnuplot"
   if (!m) nrerror("allocation failure 1 in matrix()");  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   m += NR_END;  #define FILENAMELENGTH 132
   m -= nrl;  
    #define GLOCK_ERROR_NOPATH              -1      /* empty path */
    #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  #define NINTERVMAX 8
    #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
    #define NCOVMAX 8 /* Maximum number of covariates */
   /* return pointer to array of pointers to rows */  #define MAXN 20000
   return m;  #define YEARM 12. /* Number of months per year */
 }  #define AGESUP 130
   #define AGEBASE 40
 /****************** free_imatrix *************************/  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 void free_imatrix(m,nrl,nrh,ncl,nch)  #ifdef UNIX
       int **m;  #define DIRSEPARATOR '/'
       long nch,ncl,nrh,nrl;  #define CHARSEPARATOR "/"
      /* free an int matrix allocated by imatrix() */  #define ODIRSEPARATOR '\\'
 {  #else
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #define DIRSEPARATOR '\\'
   free((FREE_ARG) (m+nrl-NR_END));  #define CHARSEPARATOR "\\"
 }  #define ODIRSEPARATOR '/'
   #endif
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  /* $Id$ */
 {  /* $State$ */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;  char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
   char fullversion[]="$Revision$ $Date$"; 
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char strstart[80];
   if (!m) nrerror("allocation failure 1 in matrix()");  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   m += NR_END;  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   m -= nrl;  int nvar;
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int npar=NPARMAX;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int nlstate=2; /* Number of live states */
   m[nrl] += NR_END;  int ndeath=1; /* Number of dead states */
   m[nrl] -= ncl;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;  int *wav; /* Number of waves for this individuual 0 is possible */
 }  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
 /*************************free matrix ************************/  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  int gipmx, gsw; /* Global variables on the number of contributions 
 {                     to the likelihood and the sum of weights (done by funcone)*/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int mle, weightopt;
   free((FREE_ARG)(m+nrl-NR_END));  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 }  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 /******************* ma3x *******************************/             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  double jmean; /* Mean space between 2 waves */
 {  double **oldm, **newm, **savm; /* Working pointers to matrices */
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   double ***m;  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int globpr; /* Global variable for printing or not */
   if (!m) nrerror("allocation failure 1 in matrix()");  double fretone; /* Only one call to likelihood */
   m += NR_END;  long ipmx; /* Number of contributions */
   m -= nrl;  double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  FILE *ficresilk;
   m[nrl] += NR_END;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   m[nrl] -= ncl;  FILE *ficresprobmorprev;
   FILE *fichtm, *fichtmcov; /* Html File */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  FILE *ficresstdeij;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  char fileresstde[FILENAMELENGTH];
   m[nrl][ncl] += NR_END;  FILE *ficrescveij;
   m[nrl][ncl] -= nll;  char filerescve[FILENAMELENGTH];
   for (j=ncl+1; j<=nch; j++)  FILE  *ficresvij;
     m[nrl][j]=m[nrl][j-1]+nlay;  char fileresv[FILENAMELENGTH];
    FILE  *ficresvpl;
   for (i=nrl+1; i<=nrh; i++) {  char fileresvpl[FILENAMELENGTH];
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  char title[MAXLINE];
     for (j=ncl+1; j<=nch; j++)  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       m[i][j]=m[i][j-1]+nlay;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   }  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   return m;  char command[FILENAMELENGTH];
 }  int  outcmd=0;
   
 /*************************free ma3x ************************/  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {  char filelog[FILENAMELENGTH]; /* Log file */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  char filerest[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  char fileregp[FILENAMELENGTH];
   free((FREE_ARG)(m+nrl-NR_END));  char popfile[FILENAMELENGTH];
 }  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 /***************** f1dim *************************/  
 extern int ncom;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 extern double *pcom,*xicom;  struct timezone tzp;
 extern double (*nrfunc)(double []);  extern int gettimeofday();
    struct tm tmg, tm, tmf, *gmtime(), *localtime();
 double f1dim(double x)  long time_value;
 {  extern long time();
   int j;  char strcurr[80], strfor[80];
   double f;  
   double *xt;  char *endptr;
    long lval;
   xt=vector(1,ncom);  double dval;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);  #define NR_END 1
   free_vector(xt,1,ncom);  #define FREE_ARG char*
   return f;  #define FTOL 1.0e-10
 }  
   #define NRANSI 
 /*****************brent *************************/  #define ITMAX 200 
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {  #define TOL 2.0e-4 
   int iter;  
   double a,b,d,etemp;  #define CGOLD 0.3819660 
   double fu,fv,fw,fx;  #define ZEPS 1.0e-10 
   double ftemp;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  #define GOLD 1.618034 
    #define GLIMIT 100.0 
   a=(ax < cx ? ax : cx);  #define TINY 1.0e-20 
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;  static double maxarg1,maxarg2;
   fw=fv=fx=(*f)(x);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   for (iter=1;iter<=ITMAX;iter++) {  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     xm=0.5*(a+b);    
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  #define rint(a) floor(a+0.5)
     printf(".");fflush(stdout);  
     fprintf(ficlog,".");fflush(ficlog);  static double sqrarg;
 #ifdef DEBUG  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     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);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
     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);  int agegomp= AGEGOMP;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif  int imx; 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  int stepm=1;
       *xmin=x;  /* Stepm, step in month: minimum step interpolation*/
       return fx;  
     }  int estepm;
     ftemp=fu;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);  int m,nb;
       q=(x-v)*(fx-fw);  long *num;
       p=(x-v)*q-(x-w)*r;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       q=2.0*(q-r);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       if (q > 0.0) p = -p;  double **pmmij, ***probs;
       q=fabs(q);  double *ageexmed,*agecens;
       etemp=e;  double dateintmean=0;
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  double *weight;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  int **s; /* Status */
       else {  double *agedc, **covar, idx;
         d=p/q;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
         u=x+d;  double *lsurv, *lpop, *tpop;
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
       }  double ftolhess; /* Tolerance for computing hessian */
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  /**************** split *************************/
     }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  {
     fu=(*f)(u);    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
     if (fu <= fx) {       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       if (u >= x) a=x; else b=x;    */ 
       SHFT(v,w,x,u)    char  *ss;                            /* pointer */
         SHFT(fv,fw,fx,fu)    int   l1, l2;                         /* length counters */
         } else {  
           if (u < x) a=u; else b=u;    l1 = strlen(path );                   /* length of path */
           if (fu <= fw || w == x) {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
             v=w;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
             w=u;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
             fv=fw;      strcpy( name, path );               /* we got the fullname name because no directory */
             fw=fu;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
           } else if (fu <= fv || v == x || v == w) {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
             v=u;      /* get current working directory */
             fv=fu;      /*    extern  char* getcwd ( char *buf , int len);*/
           }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         }        return( GLOCK_ERROR_GETCWD );
   }      }
   nrerror("Too many iterations in brent");      /* got dirc from getcwd*/
   *xmin=x;      printf(" DIRC = %s \n",dirc);
   return fx;    } else {                              /* strip direcotry from path */
 }      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
 /****************** mnbrak ***********************/      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      strncpy( dirc, path, l1 - l2 );     /* now the directory */
             double (*func)(double))      dirc[l1-l2] = 0;                    /* add zero */
 {      printf(" DIRC2 = %s \n",dirc);
   double ulim,u,r,q, dum;    }
   double fu;    /* We add a separator at the end of dirc if not exists */
      l1 = strlen( dirc );                  /* length of directory */
   *fa=(*func)(*ax);    if( dirc[l1-1] != DIRSEPARATOR ){
   *fb=(*func)(*bx);      dirc[l1] =  DIRSEPARATOR;
   if (*fb > *fa) {      dirc[l1+1] = 0; 
     SHFT(dum,*ax,*bx,dum)      printf(" DIRC3 = %s \n",dirc);
       SHFT(dum,*fb,*fa,dum)    }
       }    ss = strrchr( name, '.' );            /* find last / */
   *cx=(*bx)+GOLD*(*bx-*ax);    if (ss >0){
   *fc=(*func)(*cx);      ss++;
   while (*fb > *fc) {      strcpy(ext,ss);                     /* save extension */
     r=(*bx-*ax)*(*fb-*fc);      l1= strlen( name);
     q=(*bx-*cx)*(*fb-*fa);      l2= strlen(ss)+1;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      strncpy( finame, name, l1-l2);
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));      finame[l1-l2]= 0;
     ulim=(*bx)+GLIMIT*(*cx-*bx);    }
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);    return( 0 );                          /* we're done */
     } else if ((*cx-u)*(u-ulim) > 0.0) {  }
       fu=(*func)(u);  
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  /******************************************/
           SHFT(*fb,*fc,fu,(*func)(u))  
           }  void replace_back_to_slash(char *s, char*t)
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  {
       u=ulim;    int i;
       fu=(*func)(u);    int lg=0;
     } else {    i=0;
       u=(*cx)+GOLD*(*cx-*bx);    lg=strlen(t);
       fu=(*func)(u);    for(i=0; i<= lg; i++) {
     }      (s[i] = t[i]);
     SHFT(*ax,*bx,*cx,u)      if (t[i]== '\\') s[i]='/';
       SHFT(*fa,*fb,*fc,fu)    }
       }  }
 }  
   int nbocc(char *s, char occ)
 /*************** linmin ************************/  {
     int i,j=0;
 int ncom;    int lg=20;
 double *pcom,*xicom;    i=0;
 double (*nrfunc)(double []);    lg=strlen(s);
      for(i=0; i<= lg; i++) {
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    if  (s[i] == occ ) j++;
 {    }
   double brent(double ax, double bx, double cx,    return j;
                double (*f)(double), double tol, double *xmin);  }
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  void cutv(char *u,char *v, char*t, char occ)
               double *fc, double (*func)(double));  {
   int j;    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
   double xx,xmin,bx,ax;       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
   double fx,fb,fa;       gives u="abcedf" and v="ghi2j" */
      int i,lg,j,p=0;
   ncom=n;    i=0;
   pcom=vector(1,n);    for(j=0; j<=strlen(t)-1; j++) {
   xicom=vector(1,n);      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   nrfunc=func;    }
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];    lg=strlen(t);
     xicom[j]=xi[j];    for(j=0; j<p; j++) {
   }      (u[j] = t[j]);
   ax=0.0;    }
   xx=1.0;       u[p]='\0';
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);     for(j=0; j<= lg; j++) {
 #ifdef DEBUG      if (j>=(p+1))(v[j-p-1] = t[j]);
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    }
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  }
 #endif  
   for (j=1;j<=n;j++) {  /********************** nrerror ********************/
     xi[j] *= xmin;  
     p[j] += xi[j];  void nrerror(char error_text[])
   }  {
   free_vector(xicom,1,n);    fprintf(stderr,"ERREUR ...\n");
   free_vector(pcom,1,n);    fprintf(stderr,"%s\n",error_text);
 }    exit(EXIT_FAILURE);
   }
 /*************** powell ************************/  /*********************** vector *******************/
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  double *vector(int nl, int nh)
             double (*func)(double []))  {
 {    double *v;
   void linmin(double p[], double xi[], int n, double *fret,    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
               double (*func)(double []));    if (!v) nrerror("allocation failure in vector");
   int i,ibig,j;    return v-nl+NR_END;
   double del,t,*pt,*ptt,*xit;  }
   double fp,fptt;  
   double *xits;  /************************ free vector ******************/
   pt=vector(1,n);  void free_vector(double*v, int nl, int nh)
   ptt=vector(1,n);  {
   xit=vector(1,n);    free((FREE_ARG)(v+nl-NR_END));
   xits=vector(1,n);  }
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];  /************************ivector *******************************/
   for (*iter=1;;++(*iter)) {  int *ivector(long nl,long nh)
     fp=(*fret);  {
     ibig=0;    int *v;
     del=0.0;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    if (!v) nrerror("allocation failure in ivector");
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    return v-nl+NR_END;
     for (i=1;i<=n;i++)  }
       printf(" %d %.12f",i, p[i]);  
     fprintf(ficlog," %d %.12f",i, p[i]);  /******************free ivector **************************/
     printf("\n");  void free_ivector(int *v, long nl, long nh)
     fprintf(ficlog,"\n");  {
     for (i=1;i<=n;i++) {    free((FREE_ARG)(v+nl-NR_END));
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  }
       fptt=(*fret);  
 #ifdef DEBUG  /************************lvector *******************************/
       printf("fret=%lf \n",*fret);  long *lvector(long nl,long nh)
       fprintf(ficlog,"fret=%lf \n",*fret);  {
 #endif    long *v;
       printf("%d",i);fflush(stdout);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       fprintf(ficlog,"%d",i);fflush(ficlog);    if (!v) nrerror("allocation failure in ivector");
       linmin(p,xit,n,fret,func);    return v-nl+NR_END;
       if (fabs(fptt-(*fret)) > del) {  }
         del=fabs(fptt-(*fret));  
         ibig=i;  /******************free lvector **************************/
       }  void free_lvector(long *v, long nl, long nh)
 #ifdef DEBUG  {
       printf("%d %.12e",i,(*fret));    free((FREE_ARG)(v+nl-NR_END));
       fprintf(ficlog,"%d %.12e",i,(*fret));  }
       for (j=1;j<=n;j++) {  
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  /******************* imatrix *******************************/
         printf(" x(%d)=%.12e",j,xit[j]);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       }  { 
       for(j=1;j<=n;j++) {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
         printf(" p=%.12e",p[j]);    int **m; 
         fprintf(ficlog," p=%.12e",p[j]);    
       }    /* allocate pointers to rows */ 
       printf("\n");    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       fprintf(ficlog,"\n");    if (!m) nrerror("allocation failure 1 in matrix()"); 
 #endif    m += NR_END; 
     }    m -= nrl; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    
 #ifdef DEBUG    
       int k[2],l;    /* allocate rows and set pointers to them */ 
       k[0]=1;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       k[1]=-1;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       printf("Max: %.12e",(*func)(p));    m[nrl] += NR_END; 
       fprintf(ficlog,"Max: %.12e",(*func)(p));    m[nrl] -= ncl; 
       for (j=1;j<=n;j++) {    
         printf(" %.12e",p[j]);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
         fprintf(ficlog," %.12e",p[j]);    
       }    /* return pointer to array of pointers to rows */ 
       printf("\n");    return m; 
       fprintf(ficlog,"\n");  } 
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {  /****************** free_imatrix *************************/
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  void free_imatrix(m,nrl,nrh,ncl,nch)
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);        int **m;
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);        long nch,ncl,nrh,nrl; 
         }       /* free an int matrix allocated by imatrix() */ 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  { 
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       }    free((FREE_ARG) (m+nrl-NR_END)); 
 #endif  } 
   
   /******************* matrix *******************************/
       free_vector(xit,1,n);  double **matrix(long nrl, long nrh, long ncl, long nch)
       free_vector(xits,1,n);  {
       free_vector(ptt,1,n);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       free_vector(pt,1,n);    double **m;
       return;  
     }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    if (!m) nrerror("allocation failure 1 in matrix()");
     for (j=1;j<=n;j++) {    m += NR_END;
       ptt[j]=2.0*p[j]-pt[j];    m -= nrl;
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     fptt=(*func)(ptt);    m[nrl] += NR_END;
     if (fptt < fp) {    m[nrl] -= ncl;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         linmin(p,xit,n,fret,func);    return m;
         for (j=1;j<=n;j++) {    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
           xi[j][ibig]=xi[j][n];     */
           xi[j][n]=xit[j];  }
         }  
 #ifdef DEBUG  /*************************free matrix ************************/
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  {
         for(j=1;j<=n;j++){    free((FREE_ARG)(m[nrl]+ncl-NR_END));
           printf(" %.12e",xit[j]);    free((FREE_ARG)(m+nrl-NR_END));
           fprintf(ficlog," %.12e",xit[j]);  }
         }  
         printf("\n");  /******************* ma3x *******************************/
         fprintf(ficlog,"\n");  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 #endif  {
       }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     }    double ***m;
   }  
 }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 /**** Prevalence limit ****************/    m += NR_END;
     m -= nrl;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  
 {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      matrix by transitions matrix until convergence is reached */    m[nrl] += NR_END;
     m[nrl] -= ncl;
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   double **newm;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   double agefin, delaymax=50 ; /* Max number of years to converge */    m[nrl][ncl] += NR_END;
     m[nrl][ncl] -= nll;
   for (ii=1;ii<=nlstate+ndeath;ii++)    for (j=ncl+1; j<=nch; j++) 
     for (j=1;j<=nlstate+ndeath;j++){      m[nrl][j]=m[nrl][j-1]+nlay;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    
     }    for (i=nrl+1; i<=nrh; i++) {
       m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
    cov[1]=1.;      for (j=ncl+1; j<=nch; j++) 
          m[i][j]=m[i][j-1]+nlay;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    }
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    return m; 
     newm=savm;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     /* Covariates have to be included here again */             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
      cov[2]=agefin;    */
    }
       for (k=1; k<=cptcovn;k++) {  
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /*************************free ma3x ************************/
         /*      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]]);*/  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       }  {
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       for (k=1; k<=cptcovprod;k++)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    free((FREE_ARG)(m+nrl-NR_END));
   }
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  /*************** function subdirf ***********/
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  char *subdirf(char fileres[])
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  {
     /* Caution optionfilefiname is hidden */
     savm=oldm;    strcpy(tmpout,optionfilefiname);
     oldm=newm;    strcat(tmpout,"/"); /* Add to the right */
     maxmax=0.;    strcat(tmpout,fileres);
     for(j=1;j<=nlstate;j++){    return tmpout;
       min=1.;  }
       max=0.;  
       for(i=1; i<=nlstate; i++) {  /*************** function subdirf2 ***********/
         sumnew=0;  char *subdirf2(char fileres[], char *preop)
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  {
         prlim[i][j]= newm[i][j]/(1-sumnew);    
         max=FMAX(max,prlim[i][j]);    /* Caution optionfilefiname is hidden */
         min=FMIN(min,prlim[i][j]);    strcpy(tmpout,optionfilefiname);
       }    strcat(tmpout,"/");
       maxmin=max-min;    strcat(tmpout,preop);
       maxmax=FMAX(maxmax,maxmin);    strcat(tmpout,fileres);
     }    return tmpout;
     if(maxmax < ftolpl){  }
       return prlim;  
     }  /*************** function subdirf3 ***********/
   }  char *subdirf3(char fileres[], char *preop, char *preop2)
 }  {
     
 /*************** transition probabilities ***************/    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    strcat(tmpout,"/");
 {    strcat(tmpout,preop);
   double s1, s2;    strcat(tmpout,preop2);
   /*double t34;*/    strcat(tmpout,fileres);
   int i,j,j1, nc, ii, jj;    return tmpout;
   }
     for(i=1; i<= nlstate; i++){  
     for(j=1; j<i;j++){  /***************** f1dim *************************/
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  extern int ncom; 
         /*s2 += param[i][j][nc]*cov[nc];*/  extern double *pcom,*xicom;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  extern double (*nrfunc)(double []); 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/   
       }  double f1dim(double x) 
       ps[i][j]=s2;  { 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    int j; 
     }    double f;
     for(j=i+1; j<=nlstate+ndeath;j++){    double *xt; 
       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];    xt=vector(1,ncom); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       }    f=(*nrfunc)(xt); 
       ps[i][j]=s2;    free_vector(xt,1,ncom); 
     }    return f; 
   }  } 
     /*ps[3][2]=1;*/  
   /*****************brent *************************/
   for(i=1; i<= nlstate; i++){  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
      s1=0;  { 
     for(j=1; j<i; j++)    int iter; 
       s1+=exp(ps[i][j]);    double a,b,d,etemp;
     for(j=i+1; j<=nlstate+ndeath; j++)    double fu,fv,fw,fx;
       s1+=exp(ps[i][j]);    double ftemp;
     ps[i][i]=1./(s1+1.);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     for(j=1; j<i; j++)    double e=0.0; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];   
     for(j=i+1; j<=nlstate+ndeath; j++)    a=(ax < cx ? ax : cx); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    b=(ax > cx ? ax : cx); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    x=w=v=bx; 
   } /* end i */    fw=fv=fx=(*f)(x); 
     for (iter=1;iter<=ITMAX;iter++) { 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      xm=0.5*(a+b); 
     for(jj=1; jj<= nlstate+ndeath; jj++){      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       ps[ii][jj]=0;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       ps[ii][ii]=1;      printf(".");fflush(stdout);
     }      fprintf(ficlog,".");fflush(ficlog);
   }  #ifdef DEBUG
       printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     for(jj=1; jj<= nlstate+ndeath; jj++){  #endif
      printf("%lf ",ps[ii][jj]);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
    }        *xmin=x; 
     printf("\n ");        return fx; 
     }      } 
     printf("\n ");printf("%lf ",cov[2]);*/      ftemp=fu;
 /*      if (fabs(e) > tol1) { 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        r=(x-w)*(fx-fv); 
   goto end;*/        q=(x-v)*(fx-fw); 
     return ps;        p=(x-v)*q-(x-w)*r; 
 }        q=2.0*(q-r); 
         if (q > 0.0) p = -p; 
 /**************** Product of 2 matrices ******************/        q=fabs(q); 
         etemp=e; 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        e=d; 
 {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        else { 
   /* in, b, out are matrice of pointers which should have been initialized          d=p/q; 
      before: only the contents of out is modified. The function returns          u=x+d; 
      a pointer to pointers identical to out */          if (u-a < tol2 || b-u < tol2) 
   long i, j, k;            d=SIGN(tol1,xm-x); 
   for(i=nrl; i<= nrh; i++)        } 
     for(k=ncolol; k<=ncoloh; k++)      } else { 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         out[i][k] +=in[i][j]*b[j][k];      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   return out;      fu=(*f)(u); 
 }      if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
         SHFT(v,w,x,u) 
 /************* Higher Matrix Product ***************/          SHFT(fv,fw,fx,fu) 
           } else { 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )            if (u < x) a=u; else b=u; 
 {            if (fu <= fw || w == x) { 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month              v=w; 
      duration (i.e. until              w=u; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.              fv=fw; 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step              fw=fu; 
      (typically every 2 years instead of every month which is too big).            } else if (fu <= fv || v == x || v == w) { 
      Model is determined by parameters x and covariates have to be              v=u; 
      included manually here.              fv=fu; 
             } 
      */          } 
     } 
   int i, j, d, h, k;    nrerror("Too many iterations in brent"); 
   double **out, cov[NCOVMAX];    *xmin=x; 
   double **newm;    return fx; 
   } 
   /* Hstepm could be zero and should return the unit matrix */  
   for (i=1;i<=nlstate+ndeath;i++)  /****************** mnbrak ***********************/
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       po[i][j][0]=(i==j ? 1.0 : 0.0);              double (*func)(double)) 
     }  { 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    double ulim,u,r,q, dum;
   for(h=1; h <=nhstepm; h++){    double fu; 
     for(d=1; d <=hstepm; d++){   
       newm=savm;    *fa=(*func)(*ax); 
       /* Covariates have to be included here again */    *fb=(*func)(*bx); 
       cov[1]=1.;    if (*fb > *fa) { 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      SHFT(dum,*ax,*bx,dum) 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        SHFT(dum,*fb,*fa,dum) 
       for (k=1; k<=cptcovage;k++)        } 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    *cx=(*bx)+GOLD*(*bx-*ax); 
       for (k=1; k<=cptcovprod;k++)    *fc=(*func)(*cx); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      ulim=(*bx)+GLIMIT*(*cx-*bx); 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      if ((*bx-u)*(u-*cx) > 0.0) { 
       savm=oldm;        fu=(*func)(u); 
       oldm=newm;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     }        fu=(*func)(u); 
     for(i=1; i<=nlstate+ndeath; i++)        if (fu < *fc) { 
       for(j=1;j<=nlstate+ndeath;j++) {          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         po[i][j][h]=newm[i][j];            SHFT(*fb,*fc,fu,(*func)(u)) 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);            } 
          */      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       }        u=ulim; 
   } /* end h */        fu=(*func)(u); 
   return po;      } else { 
 }        u=(*cx)+GOLD*(*cx-*bx); 
         fu=(*func)(u); 
       } 
 /*************** log-likelihood *************/      SHFT(*ax,*bx,*cx,u) 
 double func( double *x)        SHFT(*fa,*fb,*fc,fu) 
 {        } 
   int i, ii, j, k, mi, d, kk;  } 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;  /*************** linmin ************************/
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */  int ncom; 
   long ipmx;  double *pcom,*xicom;
   /*extern weight */  double (*nrfunc)(double []); 
   /* We are differentiating ll according to initial status */   
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   /*for(i=1;i<imx;i++)  { 
     printf(" %d\n",s[4][i]);    double brent(double ax, double bx, double cx, 
   */                 double (*f)(double), double tol, double *xmin); 
   cov[1]=1.;    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   for(k=1; k<=nlstate; k++) ll[k]=0.;                double *fc, double (*func)(double)); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    int j; 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    double xx,xmin,bx,ax; 
     for(mi=1; mi<= wav[i]-1; mi++){    double fx,fb,fa;
       for (ii=1;ii<=nlstate+ndeath;ii++)   
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    ncom=n; 
       for(d=0; d<dh[mi][i]; d++){    pcom=vector(1,n); 
         newm=savm;    xicom=vector(1,n); 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    nrfunc=func; 
         for (kk=1; kk<=cptcovage;kk++) {    for (j=1;j<=n;j++) { 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      pcom[j]=p[j]; 
         }      xicom[j]=xi[j]; 
            } 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    ax=0.0; 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    xx=1.0; 
         savm=oldm;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         oldm=newm;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
          #ifdef DEBUG
            printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       } /* end mult */    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
        #endif
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    for (j=1;j<=n;j++) { 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      xi[j] *= xmin; 
       ipmx +=1;      p[j] += xi[j]; 
       sw += weight[i];    } 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    free_vector(xicom,1,n); 
     } /* end of wave */    free_vector(pcom,1,n); 
   } /* end of individual */  } 
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  char *asc_diff_time(long time_sec, char ascdiff[])
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  {
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    long sec_left, days, hours, minutes;
   return -l;    days = (time_sec) / (60*60*24);
 }    sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
     sec_left = (sec_left) %(60*60);
 /*********** Maximum Likelihood Estimation ***************/    minutes = (sec_left) /60;
     sec_left = (sec_left) % (60);
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
 {    return ascdiff;
   int i,j, iter;  }
   double **xi,*delti;  
   double fret;  /*************** powell ************************/
   xi=matrix(1,npar,1,npar);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   for (i=1;i<=npar;i++)              double (*func)(double [])) 
     for (j=1;j<=npar;j++)  { 
       xi[i][j]=(i==j ? 1.0 : 0.0);    void linmin(double p[], double xi[], int n, double *fret, 
   printf("Powell\n");  fprintf(ficlog,"Powell\n");                double (*func)(double [])); 
   powell(p,xi,npar,ftol,&iter,&fret,func);    int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    double fp,fptt;
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    double *xits;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    int niterf, itmp;
   
 }    pt=vector(1,n); 
     ptt=vector(1,n); 
 /**** Computes Hessian and covariance matrix ***/    xit=vector(1,n); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    xits=vector(1,n); 
 {    *fret=(*func)(p); 
   double  **a,**y,*x,pd;    for (j=1;j<=n;j++) pt[j]=p[j]; 
   double **hess;    for (*iter=1;;++(*iter)) { 
   int i, j,jk;      fp=(*fret); 
   int *indx;      ibig=0; 
       del=0.0; 
   double hessii(double p[], double delta, int theta, double delti[]);      last_time=curr_time;
   double hessij(double p[], double delti[], int i, int j);      (void) gettimeofday(&curr_time,&tzp);
   void lubksb(double **a, int npar, int *indx, double b[]) ;      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);
   void ludcmp(double **a, int npar, int *indx, double *d) ;      /*    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
       fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   hess=matrix(1,npar,1,npar);      */
      for (i=1;i<=n;i++) {
   printf("\nCalculation of the hessian matrix. Wait...\n");        printf(" %d %.12f",i, p[i]);
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");        fprintf(ficlog," %d %.12lf",i, p[i]);
   for (i=1;i<=npar;i++){        fprintf(ficrespow," %.12lf", p[i]);
     printf("%d",i);fflush(stdout);      }
     fprintf(ficlog,"%d",i);fflush(ficlog);      printf("\n");
     hess[i][i]=hessii(p,ftolhess,i,delti);      fprintf(ficlog,"\n");
     /*printf(" %f ",p[i]);*/      fprintf(ficrespow,"\n");fflush(ficrespow);
     /*printf(" %lf ",hess[i][i]);*/      if(*iter <=3){
   }        tm = *localtime(&curr_time.tv_sec);
          strcpy(strcurr,asctime(&tm));
   for (i=1;i<=npar;i++) {  /*       asctime_r(&tm,strcurr); */
     for (j=1;j<=npar;j++)  {        forecast_time=curr_time; 
       if (j>i) {        itmp = strlen(strcurr);
         printf(".%d%d",i,j);fflush(stdout);        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);          strcurr[itmp-1]='\0';
         hess[i][j]=hessij(p,delti,i,j);        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         hess[j][i]=hess[i][j];            fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         /*printf(" %lf ",hess[i][j]);*/        for(niterf=10;niterf<=30;niterf+=10){
       }          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
     }          tmf = *localtime(&forecast_time.tv_sec);
   }  /*      asctime_r(&tmf,strfor); */
   printf("\n");          strcpy(strfor,asctime(&tmf));
   fprintf(ficlog,"\n");          itmp = strlen(strfor);
           if(strfor[itmp-1]=='\n')
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          strfor[itmp-1]='\0';
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");          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);
            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);
   a=matrix(1,npar,1,npar);        }
   y=matrix(1,npar,1,npar);      }
   x=vector(1,npar);      for (i=1;i<=n;i++) { 
   indx=ivector(1,npar);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   for (i=1;i<=npar;i++)        fptt=(*fret); 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  #ifdef DEBUG
   ludcmp(a,npar,indx,&pd);        printf("fret=%lf \n",*fret);
         fprintf(ficlog,"fret=%lf \n",*fret);
   for (j=1;j<=npar;j++) {  #endif
     for (i=1;i<=npar;i++) x[i]=0;        printf("%d",i);fflush(stdout);
     x[j]=1;        fprintf(ficlog,"%d",i);fflush(ficlog);
     lubksb(a,npar,indx,x);        linmin(p,xit,n,fret,func); 
     for (i=1;i<=npar;i++){        if (fabs(fptt-(*fret)) > del) { 
       matcov[i][j]=x[i];          del=fabs(fptt-(*fret)); 
     }          ibig=i; 
   }        } 
   #ifdef DEBUG
   printf("\n#Hessian matrix#\n");        printf("%d %.12e",i,(*fret));
   fprintf(ficlog,"\n#Hessian matrix#\n");        fprintf(ficlog,"%d %.12e",i,(*fret));
   for (i=1;i<=npar;i++) {        for (j=1;j<=n;j++) {
     for (j=1;j<=npar;j++) {          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       printf("%.3e ",hess[i][j]);          printf(" x(%d)=%.12e",j,xit[j]);
       fprintf(ficlog,"%.3e ",hess[i][j]);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     }        }
     printf("\n");        for(j=1;j<=n;j++) {
     fprintf(ficlog,"\n");          printf(" p=%.12e",p[j]);
   }          fprintf(ficlog," p=%.12e",p[j]);
         }
   /* Recompute Inverse */        printf("\n");
   for (i=1;i<=npar;i++)        fprintf(ficlog,"\n");
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  #endif
   ludcmp(a,npar,indx,&pd);      } 
       if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   /*  printf("\n#Hessian matrix recomputed#\n");  #ifdef DEBUG
         int k[2],l;
   for (j=1;j<=npar;j++) {        k[0]=1;
     for (i=1;i<=npar;i++) x[i]=0;        k[1]=-1;
     x[j]=1;        printf("Max: %.12e",(*func)(p));
     lubksb(a,npar,indx,x);        fprintf(ficlog,"Max: %.12e",(*func)(p));
     for (i=1;i<=npar;i++){        for (j=1;j<=n;j++) {
       y[i][j]=x[i];          printf(" %.12e",p[j]);
       printf("%.3e ",y[i][j]);          fprintf(ficlog," %.12e",p[j]);
       fprintf(ficlog,"%.3e ",y[i][j]);        }
     }        printf("\n");
     printf("\n");        fprintf(ficlog,"\n");
     fprintf(ficlog,"\n");        for(l=0;l<=1;l++) {
   }          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]);
   free_matrix(a,1,npar,1,npar);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   free_matrix(y,1,npar,1,npar);          }
   free_vector(x,1,npar);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   free_ivector(indx,1,npar);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   free_matrix(hess,1,npar,1,npar);        }
   #endif
   
 }  
         free_vector(xit,1,n); 
 /*************** hessian matrix ****************/        free_vector(xits,1,n); 
 double hessii( double x[], double delta, int theta, double delti[])        free_vector(ptt,1,n); 
 {        free_vector(pt,1,n); 
   int i;        return; 
   int l=1, lmax=20;      } 
   double k1,k2;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   double p2[NPARMAX+1];      for (j=1;j<=n;j++) { 
   double res;        ptt[j]=2.0*p[j]-pt[j]; 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        xit[j]=p[j]-pt[j]; 
   double fx;        pt[j]=p[j]; 
   int k=0,kmax=10;      } 
   double l1;      fptt=(*func)(ptt); 
       if (fptt < fp) { 
   fx=func(x);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   for (i=1;i<=npar;i++) p2[i]=x[i];        if (t < 0.0) { 
   for(l=0 ; l <=lmax; l++){          linmin(p,xit,n,fret,func); 
     l1=pow(10,l);          for (j=1;j<=n;j++) { 
     delts=delt;            xi[j][ibig]=xi[j][n]; 
     for(k=1 ; k <kmax; k=k+1){            xi[j][n]=xit[j]; 
       delt = delta*(l1*k);          }
       p2[theta]=x[theta] +delt;  #ifdef DEBUG
       k1=func(p2)-fx;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       p2[theta]=x[theta]-delt;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       k2=func(p2)-fx;          for(j=1;j<=n;j++){
       /*res= (k1-2.0*fx+k2)/delt/delt; */            printf(" %.12e",xit[j]);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */            fprintf(ficlog," %.12e",xit[j]);
                }
 #ifdef DEBUG          printf("\n");
       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,"\n");
       fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  #endif
 #endif        }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      } 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    } 
         k=kmax;  } 
       }  
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  /**** Prevalence limit (stable or period prevalence)  ****************/
         k=kmax; l=lmax*10.;  
       }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  {
         delts=delt;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       }       matrix by transitions matrix until convergence is reached */
     }  
   }    int i, ii,j,k;
   delti[theta]=delts;    double min, max, maxmin, maxmax,sumnew=0.;
   return res;    double **matprod2();
      double **out, cov[NCOVMAX], **pmij();
 }    double **newm;
     double agefin, delaymax=50 ; /* Max number of years to converge */
 double hessij( double x[], double delti[], int thetai,int thetaj)  
 {    for (ii=1;ii<=nlstate+ndeath;ii++)
   int i;      for (j=1;j<=nlstate+ndeath;j++){
   int l=1, l1, lmax=20;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double k1,k2,k3,k4,res,fx;      }
   double p2[NPARMAX+1];  
   int k;     cov[1]=1.;
    
   fx=func(x);   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for (k=1; k<=2; k++) {    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     for (i=1;i<=npar;i++) p2[i]=x[i];      newm=savm;
     p2[thetai]=x[thetai]+delti[thetai]/k;      /* Covariates have to be included here again */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;       cov[2]=agefin;
     k1=func(p2)-fx;    
          for (k=1; k<=cptcovn;k++) {
     p2[thetai]=x[thetai]+delti[thetai]/k;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     p2[thetaj]=x[thetaj]-delti[thetaj]/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]]);*/
     k2=func(p2)-fx;        }
          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     p2[thetai]=x[thetai]-delti[thetai]/k;        for (k=1; k<=cptcovprod;k++)
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     k3=func(p2)-fx;  
          /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     p2[thetai]=x[thetai]-delti[thetai]/k;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     k4=func(p2)-fx;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  
 #ifdef DEBUG      savm=oldm;
     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);      oldm=newm;
     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);      maxmax=0.;
 #endif      for(j=1;j<=nlstate;j++){
   }        min=1.;
   return res;        max=0.;
 }        for(i=1; i<=nlstate; i++) {
           sumnew=0;
 /************** Inverse of matrix **************/          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
 void ludcmp(double **a, int n, int *indx, double *d)          prlim[i][j]= newm[i][j]/(1-sumnew);
 {          max=FMAX(max,prlim[i][j]);
   int i,imax,j,k;          min=FMIN(min,prlim[i][j]);
   double big,dum,sum,temp;        }
   double *vv;        maxmin=max-min;
          maxmax=FMAX(maxmax,maxmin);
   vv=vector(1,n);      }
   *d=1.0;      if(maxmax < ftolpl){
   for (i=1;i<=n;i++) {        return prlim;
     big=0.0;      }
     for (j=1;j<=n;j++)    }
       if ((temp=fabs(a[i][j])) > big) big=temp;  }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  
     vv[i]=1.0/big;  /*************** transition probabilities ***************/ 
   }  
   for (j=1;j<=n;j++) {  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     for (i=1;i<j;i++) {  {
       sum=a[i][j];    double s1, s2;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    /*double t34;*/
       a[i][j]=sum;    int i,j,j1, nc, ii, jj;
     }  
     big=0.0;      for(i=1; i<= nlstate; i++){
     for (i=j;i<=n;i++) {        for(j=1; j<i;j++){
       sum=a[i][j];          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       for (k=1;k<j;k++)            /*s2 += param[i][j][nc]*cov[nc];*/
         sum -= a[i][k]*a[k][j];            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       a[i][j]=sum;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
       if ( (dum=vv[i]*fabs(sum)) >= big) {          }
         big=dum;          ps[i][j]=s2;
         imax=i;  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
       }        }
     }        for(j=i+1; j<=nlstate+ndeath;j++){
     if (j != imax) {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       for (k=1;k<=n;k++) {            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         dum=a[imax][k];  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
         a[imax][k]=a[j][k];          }
         a[j][k]=dum;          ps[i][j]=s2;
       }        }
       *d = -(*d);      }
       vv[imax]=vv[j];      /*ps[3][2]=1;*/
     }      
     indx[j]=imax;      for(i=1; i<= nlstate; i++){
     if (a[j][j] == 0.0) a[j][j]=TINY;        s1=0;
     if (j != n) {        for(j=1; j<i; j++)
       dum=1.0/(a[j][j]);          s1+=exp(ps[i][j]);
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        for(j=i+1; j<=nlstate+ndeath; j++)
     }          s1+=exp(ps[i][j]);
   }        ps[i][i]=1./(s1+1.);
   free_vector(vv,1,n);  /* Doesn't work */        for(j=1; j<i; j++)
 ;          ps[i][j]= exp(ps[i][j])*ps[i][i];
 }        for(j=i+1; j<=nlstate+ndeath; j++)
           ps[i][j]= exp(ps[i][j])*ps[i][i];
 void lubksb(double **a, int n, int *indx, double b[])        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
 {      } /* end i */
   int i,ii=0,ip,j;      
   double sum;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
          for(jj=1; jj<= nlstate+ndeath; jj++){
   for (i=1;i<=n;i++) {          ps[ii][jj]=0;
     ip=indx[i];          ps[ii][ii]=1;
     sum=b[ip];        }
     b[ip]=b[i];      }
     if (ii)      
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  
     else if (sum) ii=i;  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
     b[i]=sum;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   }  /*         printf("ddd %lf ",ps[ii][jj]); */
   for (i=n;i>=1;i--) {  /*       } */
     sum=b[i];  /*       printf("\n "); */
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  /*        } */
     b[i]=sum/a[i][i];  /*        printf("\n ");printf("%lf ",cov[2]); */
   }         /*
 }        for(i=1; i<= npar; i++) printf("%f ",x[i]);
         goto end;*/
 /************ Frequencies ********************/      return ps;
 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 */  
    /**************** Product of 2 matrices ******************/
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  
   int first;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   double ***freq; /* Frequencies */  {
   double *pp;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   double pos, k2, dateintsum=0,k2cpt=0;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   FILE *ficresp;    /* in, b, out are matrice of pointers which should have been initialized 
   char fileresp[FILENAMELENGTH];       before: only the contents of out is modified. The function returns
         a pointer to pointers identical to out */
   pp=vector(1,nlstate);    long i, j, k;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    for(i=nrl; i<= nrh; i++)
   strcpy(fileresp,"p");      for(k=ncolol; k<=ncoloh; k++)
   strcat(fileresp,fileres);        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   if((ficresp=fopen(fileresp,"w"))==NULL) {          out[i][k] +=in[i][j]*b[j][k];
     printf("Problem with prevalence resultfile: %s\n", fileresp);  
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);    return out;
     exit(0);  }
   }  
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;  /************* Higher Matrix Product ***************/
    
   j=cptcoveff;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  {
     /* Computes the transition matrix starting at age 'age' over 
   first=1;       'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   for(k1=1; k1<=j;k1++){       nhstepm*hstepm matrices. 
     for(i1=1; i1<=ncodemax[k1];i1++){       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       j1++;       (typically every 2 years instead of every month which is too big 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);       for the memory).
         scanf("%d", i);*/       Model is determined by parameters x and covariates have to be 
       for (i=-1; i<=nlstate+ndeath; i++)         included manually here. 
         for (jk=-1; jk<=nlstate+ndeath; jk++)    
           for(m=agemin; m <= agemax+3; m++)       */
             freq[i][jk][m]=0;  
          int i, j, d, h, k;
       dateintsum=0;    double **out, cov[NCOVMAX];
       k2cpt=0;    double **newm;
       for (i=1; i<=imx; i++) {  
         bool=1;    /* Hstepm could be zero and should return the unit matrix */
         if  (cptcovn>0) {    for (i=1;i<=nlstate+ndeath;i++)
           for (z1=1; z1<=cptcoveff; z1++)      for (j=1;j<=nlstate+ndeath;j++){
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        oldm[i][j]=(i==j ? 1.0 : 0.0);
               bool=0;        po[i][j][0]=(i==j ? 1.0 : 0.0);
         }      }
         if (bool==1) {    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
           for(m=firstpass; m<=lastpass; m++){    for(h=1; h <=nhstepm; h++){
             k2=anint[m][i]+(mint[m][i]/12.);      for(d=1; d <=hstepm; d++){
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        newm=savm;
               if(agev[m][i]==0) agev[m][i]=agemax+1;        /* Covariates have to be included here again */
               if(agev[m][i]==1) agev[m][i]=agemax+2;        cov[1]=1.;
               if (m<lastpass) {        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        for (k=1; k<=cptcovage;k++)
               }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
                      for (k=1; k<=cptcovprod;k++)
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                 dateintsum=dateintsum+k2;  
                 k2cpt++;  
               }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
             }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
           }        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
       }        savm=oldm;
                oldm=newm;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      }
       for(i=1; i<=nlstate+ndeath; i++)
       if  (cptcovn>0) {        for(j=1;j<=nlstate+ndeath;j++) {
         fprintf(ficresp, "\n#********** Variable ");          po[i][j][h]=newm[i][j];
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
         fprintf(ficresp, "**********\n#");           */
       }        }
       for(i=1; i<=nlstate;i++)    } /* end h */
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    return po;
       fprintf(ficresp, "\n");  }
        
       for(i=(int)agemin; i <= (int)agemax+3; i++){  
         if(i==(int)agemax+3){  /*************** log-likelihood *************/
           fprintf(ficlog,"Total");  double func( double *x)
         }else{  {
           if(first==1){    int i, ii, j, k, mi, d, kk;
             first=0;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
             printf("See log file for details...\n");    double **out;
           }    double sw; /* Sum of weights */
           fprintf(ficlog,"Age %d", i);    double lli; /* Individual log likelihood */
         }    int s1, s2;
         for(jk=1; jk <=nlstate ; jk++){    double bbh, survp;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    long ipmx;
             pp[jk] += freq[jk][m][i];    /*extern weight */
         }    /* We are differentiating ll according to initial status */
         for(jk=1; jk <=nlstate ; jk++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           for(m=-1, pos=0; m <=0 ; m++)    /*for(i=1;i<imx;i++) 
             pos += freq[jk][m][i];      printf(" %d\n",s[4][i]);
           if(pp[jk]>=1.e-10){    */
             if(first==1){    cov[1]=1.;
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  
             }    for(k=1; k<=nlstate; k++) ll[k]=0.;
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  
           }else{    if(mle==1){
             if(first==1)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        for(mi=1; mi<= wav[i]-1; mi++){
           }          for (ii=1;ii<=nlstate+ndeath;ii++)
         }            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(jk=1; jk <=nlstate ; jk++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            }
             pp[jk] += freq[jk][m][i];          for(d=0; d<dh[mi][i]; d++){
         }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for(jk=1,pos=0; jk <=nlstate ; jk++)            for (kk=1; kk<=cptcovage;kk++) {
           pos += pp[jk];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for(jk=1; jk <=nlstate ; jk++){            }
           if(pos>=1.e-5){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             if(first==1)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            savm=oldm;
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            oldm=newm;
           }else{          } /* end mult */
             if(first==1)        
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          /* But now since version 0.9 we anticipate for bias at large stepm.
           }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
           if( i <= (int) agemax){           * (in months) between two waves is not a multiple of stepm, we rounded to 
             if(pos>=1.e-5){           * the nearest (and in case of equal distance, to the lowest) interval but now
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
               probs[i][jk][j1]= pp[jk]/pos;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/           * 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
             else           * -stepm/2 to stepm/2 .
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);           * For stepm=1 the results are the same as for previous versions of Imach.
           }           * For stepm > 1 the results are less biased than in previous versions. 
         }           */
                  s1=s[mw[mi][i]][i];
         for(jk=-1; jk <=nlstate+ndeath; jk++)          s2=s[mw[mi+1][i]][i];
           for(m=-1; m <=nlstate+ndeath; m++)          bbh=(double)bh[mi][i]/(double)stepm; 
             if(freq[jk][m][i] !=0 ) {          /* bias bh is positive if real duration
             if(first==1)           * is higher than the multiple of stepm and negative otherwise.
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);           */
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][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]));*/
             }          if( s2 > nlstate){ 
         if(i <= (int) agemax)            /* i.e. if s2 is a death state and if the date of death is known 
           fprintf(ficresp,"\n");               then the contribution to the likelihood is the probability to 
         if(first==1)               die between last step unit time and current  step unit time, 
           printf("Others in log...\n");               which is also equal to probability to die before dh 
         fprintf(ficlog,"\n");               minus probability to die before dh-stepm . 
       }               In version up to 0.92 likelihood was computed
     }          as if date of death was unknown. Death was treated as any other
   }          health state: the date of the interview describes the actual state
   dateintmean=dateintsum/k2cpt;          and not the date of a change in health state. The former idea was
            to consider that at each interview the state was recorded
   fclose(ficresp);          (healthy, disable or death) and IMaCh was corrected; but when we
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          introduced the exact date of death then we should have modified
   free_vector(pp,1,nlstate);          the contribution of an exact death to the likelihood. This new
            contribution is smaller and very dependent of the step unit
   /* End of Freq */          stepm. It is no more the probability to die between last interview
 }          and month of death but the probability to survive from last
           interview up to one month before death multiplied by the
 /************ Prevalence ********************/          probability to die within a month. Thanks to Chris
 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)          Jackson for correcting this bug.  Former versions increased
 {  /* Some frequencies */          mortality artificially. The bad side is that we add another loop
            which slows down the processing. The difference can be up to 10%
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          lower mortality.
   double ***freq; /* Frequencies */            */
   double *pp;            lli=log(out[s1][s2] - savm[s1][s2]);
   double pos, k2;  
   
   pp=vector(1,nlstate);          } else if  (s2==-2) {
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            for (j=1,survp=0. ; j<=nlstate; j++) 
                survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            /*survp += out[s1][j]; */
   j1=0;            lli= log(survp);
            }
   j=cptcoveff;          
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          else if  (s2==-4) { 
              for (j=3,survp=0. ; j<=nlstate; j++)  
   for(k1=1; k1<=j;k1++){              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     for(i1=1; i1<=ncodemax[k1];i1++){            lli= log(survp); 
       j1++;          } 
        
       for (i=-1; i<=nlstate+ndeath; i++)            else if  (s2==-5) { 
         for (jk=-1; jk<=nlstate+ndeath; jk++)              for (j=1,survp=0. ; j<=2; j++)  
           for(m=agemin; m <= agemax+3; m++)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             freq[i][jk][m]=0;            lli= log(survp); 
                } 
       for (i=1; i<=imx; i++) {          
         bool=1;          else{
         if  (cptcovn>0) {            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           for (z1=1; z1<=cptcoveff; z1++)            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          } 
               bool=0;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         }          /*if(lli ==000.0)*/
         if (bool==1) {          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
           for(m=firstpass; m<=lastpass; m++){          ipmx +=1;
             k2=anint[m][i]+(mint[m][i]/12.);          sw += weight[i];
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
               if(agev[m][i]==0) agev[m][i]=agemax+1;        } /* end of wave */
               if(agev[m][i]==1) agev[m][i]=agemax+2;      } /* end of individual */
               if (m<lastpass) {    }  else if(mle==2){
                 if (calagedate>0)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
                 else        for(mi=1; mi<= wav[i]-1; mi++){
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          for (ii=1;ii<=nlstate+ndeath;ii++)
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];            for (j=1;j<=nlstate+ndeath;j++){
               }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }            }
         }          for(d=0; d<=dh[mi][i]; d++){
       }            newm=savm;
       for(i=(int)agemin; i <= (int)agemax+3; i++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for(jk=1; jk <=nlstate ; jk++){            for (kk=1; kk<=cptcovage;kk++) {
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             pp[jk] += freq[jk][m][i];            }
         }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for(jk=1; jk <=nlstate ; jk++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           for(m=-1, pos=0; m <=0 ; m++)            savm=oldm;
             pos += freq[jk][m][i];            oldm=newm;
         }          } /* end mult */
                
         for(jk=1; jk <=nlstate ; jk++){          s1=s[mw[mi][i]][i];
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          s2=s[mw[mi+1][i]][i];
             pp[jk] += freq[jk][m][i];          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 */
                  ipmx +=1;
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          sw += weight[i];
                  ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for(jk=1; jk <=nlstate ; jk++){            } /* end of wave */
           if( i <= (int) agemax){      } /* end of individual */
             if(pos>=1.e-5){    }  else if(mle==3){  /* exponential inter-extrapolation */
               probs[i][jk][j1]= pp[jk]/pos;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           }        for(mi=1; mi<= wav[i]-1; mi++){
         }/* end jk */          for (ii=1;ii<=nlstate+ndeath;ii++)
       }/* end i */            for (j=1;j<=nlstate+ndeath;j++){
     } /* end i1 */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   } /* end k1 */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
            for(d=0; d<dh[mi][i]; d++){
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            newm=savm;
   free_vector(pp,1,nlstate);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
 }  /* End of Freq */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
 /************* Waves Concatenation ***************/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            savm=oldm;
 {            oldm=newm;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          } /* end mult */
      Death is a valid wave (if date is known).        
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          s1=s[mw[mi][i]][i];
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          s2=s[mw[mi+1][i]][i];
      and mw[mi+1][i]. dh depends on stepm.          bbh=(double)bh[mi][i]/(double)stepm; 
      */          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
           ipmx +=1;
   int i, mi, m;          sw += weight[i];
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      double sum=0., jmean=0.;*/        } /* end of wave */
   int first;      } /* end of individual */
   int j, k=0,jk, ju, jl;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   double sum=0.;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   first=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   jmin=1e+5;        for(mi=1; mi<= wav[i]-1; mi++){
   jmax=-1;          for (ii=1;ii<=nlstate+ndeath;ii++)
   jmean=0.;            for (j=1;j<=nlstate+ndeath;j++){
   for(i=1; i<=imx; i++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     mi=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     m=firstpass;            }
     while(s[m][i] <= nlstate){          for(d=0; d<dh[mi][i]; d++){
       if(s[m][i]>=1)            newm=savm;
         mw[++mi][i]=m;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if(m >=lastpass)            for (kk=1; kk<=cptcovage;kk++) {
         break;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       else            }
         m++;          
     }/* end while */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     if (s[m][i] > nlstate){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       mi++;     /* Death is another wave */            savm=oldm;
       /* if(mi==0)  never been interviewed correctly before death */            oldm=newm;
          /* Only death is a correct wave */          } /* end mult */
       mw[mi][i]=m;        
     }          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
     wav[i]=mi;          if( s2 > nlstate){ 
     if(mi==0){            lli=log(out[s1][s2] - savm[s1][s2]);
       if(first==0){          }else{
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         first=1;          }
       }          ipmx +=1;
       if(first==1){          sw += weight[i];
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],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]); */
     } /* end mi==0 */        } /* end of wave */
   }      } /* end of individual */
     }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   for(i=1; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(mi=1; mi<wav[i];mi++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       if (stepm <=0)        for(mi=1; mi<= wav[i]-1; mi++){
         dh[mi][i]=1;          for (ii=1;ii<=nlstate+ndeath;ii++)
       else{            for (j=1;j<=nlstate+ndeath;j++){
         if (s[mw[mi+1][i]][i] > nlstate) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           if (agedc[i] < 2*AGESUP) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);            }
           if(j==0) j=1;  /* Survives at least one month after exam */          for(d=0; d<dh[mi][i]; d++){
           k=k+1;            newm=savm;
           if (j >= jmax) jmax=j;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           if (j <= jmin) jmin=j;            for (kk=1; kk<=cptcovage;kk++) {
           sum=sum+j;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           /*if (j<0) printf("j=%d num=%d \n",j,i); */            }
           }          
         }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         else{                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            savm=oldm;
           k=k+1;            oldm=newm;
           if (j >= jmax) jmax=j;          } /* end mult */
           else if (j <= jmin)jmin=j;        
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          s1=s[mw[mi][i]][i];
           sum=sum+j;          s2=s[mw[mi+1][i]][i];
         }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         jk= j/stepm;          ipmx +=1;
         jl= j -jk*stepm;          sw += weight[i];
         ju= j -(jk+1)*stepm;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         if(jl <= -ju)          /*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]);*/
           dh[mi][i]=jk;        } /* end of wave */
         else      } /* end of individual */
           dh[mi][i]=jk+1;    } /* End of if */
         if(dh[mi][i]==0)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           dh[mi][i]=1; /* At least one step */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     }    return -l;
   }  }
   jmean=sum/k;  
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  /*************** log-likelihood *************/
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  double funcone( double *x)
  }  {
     /* Same as likeli but slower because of a lot of printf and if */
 /*********** Tricode ****************************/    int i, ii, j, k, mi, d, kk;
 void tricode(int *Tvar, int **nbcode, int imx)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
 {    double **out;
   int Ndum[20],ij=1, k, j, i;    double lli; /* Individual log likelihood */
   int cptcode=0;    double llt;
   cptcoveff=0;    int s1, s2;
      double bbh, survp;
   for (k=0; k<19; k++) Ndum[k]=0;    /*extern weight */
   for (k=1; k<=7; k++) ncodemax[k]=0;    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    /*for(i=1;i<imx;i++) 
     for (i=1; i<=imx; i++) {      printf(" %d\n",s[4][i]);
       ij=(int)(covar[Tvar[j]][i]);    */
       Ndum[ij]++;    cov[1]=1.;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  
       if (ij > cptcode) cptcode=ij;    for(k=1; k<=nlstate; k++) ll[k]=0.;
     }  
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (i=0; i<=cptcode; i++) {      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       if(Ndum[i]!=0) ncodemax[j]++;      for(mi=1; mi<= wav[i]-1; mi++){
     }        for (ii=1;ii<=nlstate+ndeath;ii++)
     ij=1;          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<=ncodemax[j]; i++) {          }
       for (k=0; k<=19; k++) {        for(d=0; d<dh[mi][i]; d++){
         if (Ndum[k] != 0) {          newm=savm;
           nbcode[Tvar[j]][ij]=k;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                    for (kk=1; kk<=cptcovage;kk++) {
           ij++;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }          }
         if (ij > ncodemax[j]) break;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }          savm=oldm;
   }            oldm=newm;
         } /* end mult */
  for (k=0; k<19; k++) Ndum[k]=0;        
         s1=s[mw[mi][i]][i];
  for (i=1; i<=ncovmodel-2; i++) {        s2=s[mw[mi+1][i]][i];
    ij=Tvar[i];        bbh=(double)bh[mi][i]/(double)stepm; 
    Ndum[ij]++;        /* bias is positive if real duration
  }         * is higher than the multiple of stepm and negative otherwise.
          */
  ij=1;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
  for (i=1; i<=10; i++) {          lli=log(out[s1][s2] - savm[s1][s2]);
    if((Ndum[i]!=0) && (i<=ncovcol)){        } else if  (s2==-2) {
      Tvaraff[ij]=i;          for (j=1,survp=0. ; j<=nlstate; j++) 
      ij++;            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
    }          lli= log(survp);
  }        }else if (mle==1){
            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
  cptcoveff=ij-1;        } else if(mle==2){
 }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         } else if(mle==3){  /* exponential inter-extrapolation */
 /*********** Health Expectancies ****************/          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         } else if (mle==4){  /* mle=4 no inter-extrapolation */
 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 )          lli=log(out[s1][s2]); /* Original formula */
         } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
 {          lli=log(out[s1][s2]); /* Original formula */
   /* Health expectancies */        } /* End of if */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;        ipmx +=1;
   double age, agelim, hf;        sw += weight[i];
   double ***p3mat,***varhe;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double **dnewm,**doldm;  /*       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]); */
   double *xp;        if(globpr){
   double **gp, **gm;          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   double ***gradg, ***trgradg;   %11.6f %11.6f %11.6f ", \
   int theta;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                   2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   xp=vector(1,npar);            llt +=ll[k]*gipmx/gsw;
   dnewm=matrix(1,nlstate*2,1,npar);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   doldm=matrix(1,nlstate*2,1,nlstate*2);          }
            fprintf(ficresilk," %10.6f\n", -llt);
   fprintf(ficreseij,"# Health expectancies\n");        }
   fprintf(ficreseij,"# Age");      } /* end of wave */
   for(i=1; i<=nlstate;i++)    } /* end of individual */
     for(j=1; j<=nlstate;j++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   fprintf(ficreseij,"\n");    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if(globpr==0){ /* First time we count the contributions and weights */
   if(estepm < stepm){      gipmx=ipmx;
     printf ("Problem %d lower than %d\n",estepm, stepm);      gsw=sw;
   }    }
   else  hstepm=estepm;      return -l;
   /* We compute the life expectancy from trapezoids spaced every estepm months  }
    * This is mainly to measure the difference between two models: for example  
    * if stepm=24 months pijx are given only every 2 years and by summing them  
    * we are calculating an estimate of the Life Expectancy assuming a linear  /*************** function likelione ***********/
    * progression inbetween and thus overestimating or underestimating according  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
    * 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    /* This routine should help understanding what is done with 
    * to compare the new estimate of Life expectancy with the same linear       the selection of individuals/waves and
    * hypothesis. A more precise result, taking into account a more precise       to check the exact contribution to the likelihood.
    * curvature will be obtained if estepm is as small as stepm. */       Plotting could be done.
      */
   /* For example we decided to compute the life expectancy with the smallest unit */    int k;
   /* 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    if(*globpri !=0){ /* Just counts and sums, no printings */
      nstepm is the number of stepm from age to agelin.      strcpy(fileresilk,"ilk"); 
      Look at hpijx to understand the reason of that which relies in memory size      strcat(fileresilk,fileres);
      and note for a fixed period like estepm months */      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        printf("Problem with resultfile: %s\n", fileresilk);
      survival function given by stepm (the optimization length). Unfortunately it        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
      means that if the survival funtion is printed only each two years of age and if      }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      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");
      results. So we changed our mind and took the option of the best precision.      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   */      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   agelim=AGESUP;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   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);    *fretone=(*funcone)(p);
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    if(*globpri !=0){
     /* if (stepm >= YEARM) hstepm=1;*/      fclose(ficresilk);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fflush(fichtm); 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    } 
     gp=matrix(0,nhstepm,1,nlstate*2);    return;
     gm=matrix(0,nhstepm,1,nlstate*2);  }
   
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  /*********** Maximum Likelihood Estimation ***************/
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    
    void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    int i,j, iter;
     double **xi;
     /* Computing Variances of health expectancies */    double fret;
     double fretone; /* Only one call to likelihood */
      for(theta=1; theta <=npar; theta++){    /*  char filerespow[FILENAMELENGTH];*/
       for(i=1; i<=npar; i++){    xi=matrix(1,npar,1,npar);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    for (i=1;i<=npar;i++)
       }      for (j=1;j<=npar;j++)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          xi[i][j]=(i==j ? 1.0 : 0.0);
      printf("Powell\n");  fprintf(ficlog,"Powell\n");
       cptj=0;    strcpy(filerespow,"pow"); 
       for(j=1; j<= nlstate; j++){    strcat(filerespow,fileres);
         for(i=1; i<=nlstate; i++){    if((ficrespow=fopen(filerespow,"w"))==NULL) {
           cptj=cptj+1;      printf("Problem with resultfile: %s\n", filerespow);
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    }
           }    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");
       for(i=1; i<=npar; i++)  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    powell(p,xi,npar,ftol,&iter,&fret,func);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
          free_matrix(xi,1,npar,1,npar);
       cptj=0;    fclose(ficrespow);
       for(j=1; j<= nlstate; j++){    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         for(i=1;i<=nlstate;i++){    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           cptj=cptj+1;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){  
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  }
           }  
         }  /**** Computes Hessian and covariance matrix ***/
       }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       for(j=1; j<= nlstate*2; j++)  {
         for(h=0; h<=nhstepm-1; h++){    double  **a,**y,*x,pd;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    double **hess;
         }    int i, j,jk;
      }    int *indx;
      
 /* End theta */    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
      for(h=0; h<=nhstepm-1; h++)    double gompertz(double p[]);
       for(j=1; j<=nlstate*2;j++)    hess=matrix(1,npar,1,npar);
         for(theta=1; theta <=npar; theta++)  
           trgradg[h][j][theta]=gradg[h][theta][j];    printf("\nCalculation of the hessian matrix. Wait...\n");
          fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
      for(i=1;i<=nlstate*2;i++)      printf("%d",i);fflush(stdout);
       for(j=1;j<=nlstate*2;j++)      fprintf(ficlog,"%d",i);fflush(ficlog);
         varhe[i][j][(int)age] =0.;     
        hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
      printf("%d|",(int)age);fflush(stdout);      
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);      /*  printf(" %f ",p[i]);
      for(h=0;h<=nhstepm-1;h++){          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       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]);    for (i=1;i<=npar;i++) {
         for(i=1;i<=nlstate*2;i++)      for (j=1;j<=npar;j++)  {
           for(j=1;j<=nlstate*2;j++)        if (j>i) { 
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;          printf(".%d%d",i,j);fflush(stdout);
       }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     }          hess[i][j]=hessij(p,delti,i,j,func,npar);
     /* Computing expectancies */          
     for(i=1; i<=nlstate;i++)          hess[j][i]=hess[i][j];    
       for(j=1; j<=nlstate;j++)          /*printf(" %lf ",hess[i][j]);*/
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){        }
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      }
              }
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/    printf("\n");
     fprintf(ficlog,"\n");
         }  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficreseij,"%3.0f",age );    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     cptj=0;    
     for(i=1; i<=nlstate;i++)    a=matrix(1,npar,1,npar);
       for(j=1; j<=nlstate;j++){    y=matrix(1,npar,1,npar);
         cptj++;    x=vector(1,npar);
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );    indx=ivector(1,npar);
       }    for (i=1;i<=npar;i++)
     fprintf(ficreseij,"\n");      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
        ludcmp(a,npar,indx,&pd);
     free_matrix(gm,0,nhstepm,1,nlstate*2);  
     free_matrix(gp,0,nhstepm,1,nlstate*2);    for (j=1;j<=npar;j++) {
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);      for (i=1;i<=npar;i++) x[i]=0;
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);      x[j]=1;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      lubksb(a,npar,indx,x);
   }      for (i=1;i<=npar;i++){ 
   printf("\n");        matcov[i][j]=x[i];
   fprintf(ficlog,"\n");      }
     }
   free_vector(xp,1,npar);  
   free_matrix(dnewm,1,nlstate*2,1,npar);    printf("\n#Hessian matrix#\n");
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);    fprintf(ficlog,"\n#Hessian matrix#\n");
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);    for (i=1;i<=npar;i++) { 
 }      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
 /************ Variance ******************/        fprintf(ficlog,"%.3e ",hess[i][j]);
 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)      }
 {      printf("\n");
   /* Variance of health expectancies */      fprintf(ficlog,"\n");
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    }
   /* double **newm;*/  
   double **dnewm,**doldm;    /* Recompute Inverse */
   double **dnewmp,**doldmp;    for (i=1;i<=npar;i++)
   int i, j, nhstepm, hstepm, h, nstepm ;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   int k, cptcode;    ludcmp(a,npar,indx,&pd);
   double *xp;  
   double **gp, **gm;  /* for var eij */    /*  printf("\n#Hessian matrix recomputed#\n");
   double ***gradg, ***trgradg; /*for var eij */  
   double **gradgp, **trgradgp; /* for var p point j */    for (j=1;j<=npar;j++) {
   double *gpp, *gmp; /* for var p point j */      for (i=1;i<=npar;i++) x[i]=0;
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */      x[j]=1;
   double ***p3mat;      lubksb(a,npar,indx,x);
   double age,agelim, hf;      for (i=1;i<=npar;i++){ 
   int theta;        y[i][j]=x[i];
   char digit[4];        printf("%.3e ",y[i][j]);
   char digitp[16];        fprintf(ficlog,"%.3e ",y[i][j]);
       }
   char fileresprobmorprev[FILENAMELENGTH];      printf("\n");
       fprintf(ficlog,"\n");
   if(popbased==1)    }
     strcpy(digitp,"-populbased-");    */
   else  
     strcpy(digitp,"-stablbased-");    free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
   strcpy(fileresprobmorprev,"prmorprev");    free_vector(x,1,npar);
   sprintf(digit,"%-d",ij);    free_ivector(indx,1,npar);
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/    free_matrix(hess,1,npar,1,npar);
   strcat(fileresprobmorprev,digit); /* Tvar to be done */  
   strcat(fileresprobmorprev,digitp); /* Popbased or not */  
   strcat(fileresprobmorprev,fileres);  }
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprobmorprev);  /*************** hessian matrix ****************/
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   }  {
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    int i;
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);    int l=1, lmax=20;
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");    double k1,k2;
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);    double p2[NPARMAX+1];
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){    double res;
     fprintf(ficresprobmorprev," p.%-d SE",j);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     for(i=1; i<=nlstate;i++)    double fx;
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);    int k=0,kmax=10;
   }      double l1;
   fprintf(ficresprobmorprev,"\n");  
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    fx=func(x);
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    for (i=1;i<=npar;i++) p2[i]=x[i];
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);    for(l=0 ; l <=lmax; l++){
     exit(0);      l1=pow(10,l);
   }      delts=delt;
   else{      for(k=1 ; k <kmax; k=k+1){
     fprintf(ficgp,"\n# Routine varevsij");        delt = delta*(l1*k);
   }        p2[theta]=x[theta] +delt;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {        k1=func(p2)-fx;
     printf("Problem with html file: %s\n", optionfilehtm);        p2[theta]=x[theta]-delt;
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);        k2=func(p2)-fx;
     exit(0);        /*res= (k1-2.0*fx+k2)/delt/delt; */
   }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   else{        
     fprintf(fichtm,"\n<li><h4> Computing step probabilities of dying and weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");  #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);
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   #endif
   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");        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   fprintf(ficresvij,"# Age");        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   for(i=1; i<=nlstate;i++)          k=kmax;
     for(j=1; j<=nlstate;j++)        }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   fprintf(ficresvij,"\n");          k=kmax; l=lmax*10.;
         }
   xp=vector(1,npar);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   dnewm=matrix(1,nlstate,1,npar);          delts=delt;
   doldm=matrix(1,nlstate,1,nlstate);        }
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);      }
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    }
     delti[theta]=delts;
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);    return res; 
   gpp=vector(nlstate+1,nlstate+ndeath);    
   gmp=vector(nlstate+1,nlstate+ndeath);  }
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/  
    double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   if(estepm < stepm){  {
     printf ("Problem %d lower than %d\n",estepm, stepm);    int i;
   }    int l=1, l1, lmax=20;
   else  hstepm=estepm;      double k1,k2,k3,k4,res,fx;
   /* For example we decided to compute the life expectancy with the smallest unit */    double p2[NPARMAX+1];
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    int k;
      nhstepm is the number of hstepm from age to agelim  
      nstepm is the number of stepm from age to agelin.    fx=func(x);
      Look at hpijx to understand the reason of that which relies in memory size    for (k=1; k<=2; k++) {
      and note for a fixed period like k years */      for (i=1;i<=npar;i++) p2[i]=x[i];
   /* 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      k1=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 */      k2=func(p2)-fx;
   agelim = AGESUP;    
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      p2[thetai]=x[thetai]-delti[thetai]/k;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      k3=func(p2)-fx;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      p2[thetai]=x[thetai]-delti[thetai]/k;
     gp=matrix(0,nhstepm,1,nlstate);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     gm=matrix(0,nhstepm,1,nlstate);      k4=func(p2)-fx;
       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
     for(theta=1; theta <=npar; theta++){      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       for(i=1; i<=npar; i++){ /* Computes gradient */      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);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  #endif
       }    }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      return res;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  }
   
       if (popbased==1) {  /************** Inverse of matrix **************/
         for(i=1; i<=nlstate;i++)  void ludcmp(double **a, int n, int *indx, double *d) 
           prlim[i][i]=probs[(int)age][i][ij];  { 
       }    int i,imax,j,k; 
      double big,dum,sum,temp; 
       for(j=1; j<= nlstate; j++){    double *vv; 
         for(h=0; h<=nhstepm; h++){   
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    vv=vector(1,n); 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    *d=1.0; 
         }    for (i=1;i<=n;i++) { 
       }      big=0.0; 
       /* This for computing forces of mortality (h=1)as a weighted average */      for (j=1;j<=n;j++) 
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){        if ((temp=fabs(a[i][j])) > big) big=temp; 
         for(i=1; i<= nlstate; i++)      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           gpp[j] += prlim[i][i]*p3mat[i][j][1];      vv[i]=1.0/big; 
       }        } 
       /* end force of mortality */    for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
       for(i=1; i<=npar; i++) /* Computes gradient */        sum=a[i][j]; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          a[i][j]=sum; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      } 
        big=0.0; 
       if (popbased==1) {      for (i=j;i<=n;i++) { 
         for(i=1; i<=nlstate;i++)        sum=a[i][j]; 
           prlim[i][i]=probs[(int)age][i][ij];        for (k=1;k<j;k++) 
       }          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
       for(j=1; j<= nlstate; j++){        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         for(h=0; h<=nhstepm; h++){          big=dum; 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          imax=i; 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        } 
         }      } 
       }      if (j != imax) { 
       /* This for computing force of mortality (h=1)as a weighted average */        for (k=1;k<=n;k++) { 
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){          dum=a[imax][k]; 
         for(i=1; i<= nlstate; i++)          a[imax][k]=a[j][k]; 
           gmp[j] += prlim[i][i]*p3mat[i][j][1];          a[j][k]=dum; 
       }            } 
       /* end force of mortality */        *d = -(*d); 
         vv[imax]=vv[j]; 
       for(j=1; j<= nlstate; j++) /* vareij */      } 
         for(h=0; h<=nhstepm; h++){      indx[j]=imax; 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      if (a[j][j] == 0.0) a[j][j]=TINY; 
         }      if (j != n) { 
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */        dum=1.0/(a[j][j]); 
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       }      } 
     } 
     } /* End theta */    free_vector(vv,1,n);  /* Doesn't work */
   ;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */  } 
   
     for(h=0; h<=nhstepm; h++) /* veij */  void lubksb(double **a, int n, int *indx, double b[]) 
       for(j=1; j<=nlstate;j++)  { 
         for(theta=1; theta <=npar; theta++)    int i,ii=0,ip,j; 
           trgradg[h][j][theta]=gradg[h][theta][j];    double sum; 
    
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */    for (i=1;i<=n;i++) { 
       for(theta=1; theta <=npar; theta++)      ip=indx[i]; 
         trgradgp[j][theta]=gradgp[theta][j];      sum=b[ip]; 
       b[ip]=b[i]; 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      if (ii) 
     for(i=1;i<=nlstate;i++)        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       for(j=1;j<=nlstate;j++)      else if (sum) ii=i; 
         vareij[i][j][(int)age] =0.;      b[i]=sum; 
     } 
     for(h=0;h<=nhstepm;h++){    for (i=n;i>=1;i--) { 
       for(k=0;k<=nhstepm;k++){      sum=b[i]; 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      b[i]=sum/a[i][i]; 
         for(i=1;i<=nlstate;i++)    } 
           for(j=1;j<=nlstate;j++)  } 
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;  
       }  void pstamp(FILE *fichier)
     }  {
     fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
     /* pptj */  }
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);  
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);  /************ Frequencies ********************/
     for(j=nlstate+1;j<=nlstate+ndeath;j++)  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, char strstart[])
       for(i=nlstate+1;i<=nlstate+ndeath;i++)  {  /* Some frequencies */
         varppt[j][i]=doldmp[j][i];    
     /* end ppptj */    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);      int first;
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);    double ***freq; /* Frequencies */
      double *pp, **prop;
     if (popbased==1) {    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       for(i=1; i<=nlstate;i++)    char fileresp[FILENAMELENGTH];
         prlim[i][i]=probs[(int)age][i][ij];    
     }    pp=vector(1,nlstate);
        prop=matrix(1,nlstate,iagemin,iagemax+3);
     /* This for computing force of mortality (h=1)as a weighted average */    strcpy(fileresp,"p");
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){    strcat(fileresp,fileres);
       for(i=1; i<= nlstate; i++)    if((ficresp=fopen(fileresp,"w"))==NULL) {
         gmp[j] += prlim[i][i]*p3mat[i][j][1];      printf("Problem with prevalence resultfile: %s\n", fileresp);
     }          fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     /* end force of mortality */      exit(0);
     }
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){    j1=0;
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));    
       for(i=1; i<=nlstate;i++){    j=cptcoveff;
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       }  
     }    first=1;
     fprintf(ficresprobmorprev,"\n");  
     for(k1=1; k1<=j;k1++){
     fprintf(ficresvij,"%.0f ",age );      for(i1=1; i1<=ncodemax[k1];i1++){
     for(i=1; i<=nlstate;i++)        j1++;
       for(j=1; j<=nlstate;j++){        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);          scanf("%d", i);*/
       }        for (i=-5; i<=nlstate+ndeath; i++)  
     fprintf(ficresvij,"\n");          for (jk=-5; jk<=nlstate+ndeath; jk++)  
     free_matrix(gp,0,nhstepm,1,nlstate);            for(m=iagemin; m <= iagemax+3; m++)
     free_matrix(gm,0,nhstepm,1,nlstate);              freq[i][jk][m]=0;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      for (i=1; i<=nlstate; i++)  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(m=iagemin; m <= iagemax+3; m++)
   } /* End age */          prop[i][m]=0;
   free_vector(gpp,nlstate+1,nlstate+ndeath);        
   free_vector(gmp,nlstate+1,nlstate+ndeath);        dateintsum=0;
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);        k2cpt=0;
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/        for (i=1; i<=imx; i++) {
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");          bool=1;
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */          if  (cptcovn>0) {
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");            for (z1=1; z1<=cptcoveff; z1++) 
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);                bool=0;
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);          }
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);          if (bool==1){
   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(m=firstpass; m<=lastpass; m++){
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);              k2=anint[m][i]+(mint[m][i]/12.);
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   free_vector(xp,1,npar);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   free_matrix(doldm,1,nlstate,1,nlstate);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   free_matrix(dnewm,1,nlstate,1,npar);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);                if (m<lastpass) {
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   fclose(ficresprobmorprev);                }
   fclose(ficgp);                
   fclose(fichtm);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
 }                  k2cpt++;
                 }
 /************ Variance of prevlim ******************/                /*}*/
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)            }
 {          }
   /* Variance of prevalence limit */        }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/         
   double **newm;        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   double **dnewm,**doldm;        pstamp(ficresp);
   int i, j, nhstepm, hstepm;        if  (cptcovn>0) {
   int k, cptcode;          fprintf(ficresp, "\n#********** Variable "); 
   double *xp;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   double *gp, *gm;          fprintf(ficresp, "**********\n#");
   double **gradg, **trgradg;        }
   double age,agelim;        for(i=1; i<=nlstate;i++) 
   int theta;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
            fprintf(ficresp, "\n");
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");        
   fprintf(ficresvpl,"# Age");        for(i=iagemin; i <= iagemax+3; i++){
   for(i=1; i<=nlstate;i++)          if(i==iagemax+3){
       fprintf(ficresvpl," %1d-%1d",i,i);            fprintf(ficlog,"Total");
   fprintf(ficresvpl,"\n");          }else{
             if(first==1){
   xp=vector(1,npar);              first=0;
   dnewm=matrix(1,nlstate,1,npar);              printf("See log file for details...\n");
   doldm=matrix(1,nlstate,1,nlstate);            }
              fprintf(ficlog,"Age %d", i);
   hstepm=1*YEARM; /* Every year of age */          }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          for(jk=1; jk <=nlstate ; jk++){
   agelim = AGESUP;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              pp[jk] += freq[jk][m][i]; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          }
     if (stepm >= YEARM) hstepm=1;          for(jk=1; jk <=nlstate ; jk++){
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            for(m=-1, pos=0; m <=0 ; m++)
     gradg=matrix(1,npar,1,nlstate);              pos += freq[jk][m][i];
     gp=vector(1,nlstate);            if(pp[jk]>=1.e-10){
     gm=vector(1,nlstate);              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     for(theta=1; theta <=npar; theta++){              }
       for(i=1; i<=npar; i++){ /* Computes gradient */              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            }else{
       }              if(first==1)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       for(i=1;i<=nlstate;i++)              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         gp[i] = prlim[i][i];            }
              }
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          for(jk=1; jk <=nlstate ; jk++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       for(i=1;i<=nlstate;i++)              pp[jk] += freq[jk][m][i];
         gm[i] = prlim[i][i];          }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       for(i=1;i<=nlstate;i++)            pos += pp[jk];
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];            posprop += prop[jk][i];
     } /* End theta */          }
           for(jk=1; jk <=nlstate ; jk++){
     trgradg =matrix(1,nlstate,1,npar);            if(pos>=1.e-5){
               if(first==1)
     for(j=1; j<=nlstate;j++)                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       for(theta=1; theta <=npar; theta++)              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         trgradg[j][theta]=gradg[theta][j];            }else{
               if(first==1)
     for(i=1;i<=nlstate;i++)                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       varpl[i][(int)age] =0.;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            }
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);            if( i <= iagemax){
     for(i=1;i<=nlstate;i++)              if(pos>=1.e-5){
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
     fprintf(ficresvpl,"%.0f ",age );                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     for(i=1; i<=nlstate;i++)              }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));              else
     fprintf(ficresvpl,"\n");                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     free_vector(gp,1,nlstate);            }
     free_vector(gm,1,nlstate);          }
     free_matrix(gradg,1,npar,1,nlstate);          
     free_matrix(trgradg,1,nlstate,1,npar);          for(jk=-1; jk <=nlstate+ndeath; jk++)
   } /* End age */            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
   free_vector(xp,1,npar);              if(first==1)
   free_matrix(doldm,1,nlstate,1,npar);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   free_matrix(dnewm,1,nlstate,1,nlstate);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
 }          if(i <= iagemax)
             fprintf(ficresp,"\n");
 /************ Variance of one-step probabilities  ******************/          if(first==1)
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)            printf("Others in log...\n");
 {          fprintf(ficlog,"\n");
   int i, j=0,  i1, k1, l1, t, tj;        }
   int k2, l2, j1,  z1;      }
   int k=0,l, cptcode;    }
   int first=1, first1;    dateintmean=dateintsum/k2cpt; 
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;   
   double **dnewm,**doldm;    fclose(ficresp);
   double *xp;    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   double *gp, *gm;    free_vector(pp,1,nlstate);
   double **gradg, **trgradg;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   double **mu;    /* End of Freq */
   double age,agelim, cov[NCOVMAX];  }
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */  
   int theta;  /************ Prevalence ********************/
   char fileresprob[FILENAMELENGTH];  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
   char fileresprobcov[FILENAMELENGTH];  {  
   char fileresprobcor[FILENAMELENGTH];    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
   double ***varpij;       We still use firstpass and lastpass as another selection.
     */
   strcpy(fileresprob,"prob");   
   strcat(fileresprob,fileres);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    double ***freq; /* Frequencies */
     printf("Problem with resultfile: %s\n", fileresprob);    double *pp, **prop;
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);    double pos,posprop; 
   }    double  y2; /* in fractional years */
   strcpy(fileresprobcov,"probcov");    int iagemin, iagemax;
   strcat(fileresprobcov,fileres);  
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {    iagemin= (int) agemin;
     printf("Problem with resultfile: %s\n", fileresprobcov);    iagemax= (int) agemax;
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);    /*pp=vector(1,nlstate);*/
   }    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   strcpy(fileresprobcor,"probcor");    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   strcat(fileresprobcor,fileres);    j1=0;
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    
     printf("Problem with resultfile: %s\n", fileresprobcor);    j=cptcoveff;
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   }    
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    for(k1=1; k1<=j;k1++){
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);      for(i1=1; i1<=ncodemax[k1];i1++){
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);        j1++;
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);        
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);        for (i=1; i<=nlstate; i++)  
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);          for(m=iagemin; m <= iagemax+3; m++)
              prop[i][m]=0.0;
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");       
   fprintf(ficresprob,"# Age");        for (i=1; i<=imx; i++) { /* Each individual */
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");          bool=1;
   fprintf(ficresprobcov,"# Age");          if  (cptcovn>0) {
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");            for (z1=1; z1<=cptcoveff; z1++) 
   fprintf(ficresprobcov,"# Age");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
           } 
   for(i=1; i<=nlstate;i++)          if (bool==1) { 
     for(j=1; j<=(nlstate+ndeath);j++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       fprintf(ficresprobcov," p%1d-%1d ",i,j);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       fprintf(ficresprobcor," p%1d-%1d ",i,j);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     }                  if(agev[m][i]==1) agev[m][i]=iagemax+2;
   fprintf(ficresprob,"\n");                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); 
   fprintf(ficresprobcov,"\n");                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   fprintf(ficresprobcor,"\n");                  /*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=vector(1,npar);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);                  prop[s[m][i]][iagemax+3] += weight[i]; 
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));                } 
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);              }
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);            } /* end selection of waves */
   first=1;          }
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {        }
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);        for(i=iagemin; i <= iagemax+3; i++){  
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);          
     exit(0);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   }            posprop += prop[jk][i]; 
   else{          } 
     fprintf(ficgp,"\n# Routine varprob");  
   }          for(jk=1; jk <=nlstate ; jk++){     
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {            if( i <=  iagemax){ 
     printf("Problem with html file: %s\n", optionfilehtm);              if(posprop>=1.e-5){ 
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);                probs[i][jk][j1]= prop[jk][i]/posprop;
     exit(0);              } 
   }            } 
   else{          }/* end jk */ 
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");        }/* end i */ 
     fprintf(fichtm,"\n");      } /* end i1 */
     } /* end k1 */
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");    
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     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");    /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  }  /* End of prevalence */
   
    /************* Waves Concatenation ***************/
   cov[1]=1;  
   tj=cptcoveff;  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)
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}  {
   j1=0;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   for(t=1; t<=tj;t++){       Death is a valid wave (if date is known).
     for(i1=1; i1<=ncodemax[t];i1++){       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       j1++;       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
             and mw[mi+1][i]. dh depends on stepm.
       if  (cptcovn>0) {       */
         fprintf(ficresprob, "\n#********** Variable ");  
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    int i, mi, m;
         fprintf(ficresprob, "**********\n#");    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         fprintf(ficresprobcov, "\n#********** Variable ");       double sum=0., jmean=0.;*/
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    int first;
         fprintf(ficresprobcov, "**********\n#");    int j, k=0,jk, ju, jl;
            double sum=0.;
         fprintf(ficgp, "\n#********** Variable ");    first=0;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    jmin=1e+5;
         fprintf(ficgp, "**********\n#");    jmax=-1;
            jmean=0.;
            for(i=1; i<=imx; i++){
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");      mi=0;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      m=firstpass;
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");      while(s[m][i] <= nlstate){
                if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
         fprintf(ficresprobcor, "\n#********** Variable ");              mw[++mi][i]=m;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        if(m >=lastpass)
         fprintf(ficgp, "**********\n#");              break;
       }        else
                m++;
       for (age=bage; age<=fage; age ++){      }/* end while */
         cov[2]=age;      if (s[m][i] > nlstate){
         for (k=1; k<=cptcovn;k++) {        mi++;     /* Death is another wave */
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];        /* if(mi==0)  never been interviewed correctly before death */
         }           /* Only death is a correct wave */
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        mw[mi][i]=m;
         for (k=1; k<=cptcovprod;k++)      }
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
              wav[i]=mi;
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));      if(mi==0){
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);        nbwarn++;
         gp=vector(1,(nlstate)*(nlstate+ndeath));        if(first==0){
         gm=vector(1,(nlstate)*(nlstate+ndeath));          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
              first=1;
         for(theta=1; theta <=npar; theta++){        }
           for(i=1; i<=npar; i++)        if(first==1){
             xp[i] = x[i] + (i==theta ?delti[theta]:0);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
                  }
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      } /* end mi==0 */
              } /* End individuals */
           k=0;  
           for(i=1; i<= (nlstate); i++){    for(i=1; i<=imx; i++){
             for(j=1; j<=(nlstate+ndeath);j++){      for(mi=1; mi<wav[i];mi++){
               k=k+1;        if (stepm <=0)
               gp[k]=pmmij[i][j];          dh[mi][i]=1;
             }        else{
           }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                      if (agedc[i] < 2*AGESUP) {
           for(i=1; i<=npar; i++)              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
             xp[i] = x[i] - (i==theta ?delti[theta]:0);              if(j==0) j=1;  /* Survives at least one month after exam */
                  else if(j<0){
           pmij(pmmij,cov,ncovmodel,xp,nlstate);                nberr++;
           k=0;                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]);
           for(i=1; i<=(nlstate); i++){                j=1; /* Temporary Dangerous patch */
             for(j=1; j<=(nlstate+ndeath);j++){                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               k=k+1;                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]);
               gm[k]=pmmij[i][j];                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
             }              }
           }              k=k+1;
                    if (j >= jmax){
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)                jmax=j;
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                  ijmax=i;
         }              }
               if (j <= jmin){
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)                jmin=j;
           for(theta=1; theta <=npar; theta++)                ijmin=i;
             trgradg[j][theta]=gradg[theta][j];              }
                      sum=sum+j;
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                    }
         pmij(pmmij,cov,ncovmodel,x,nlstate);          }
                  else{
         k=0;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         for(i=1; i<=(nlstate); i++){  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
           for(j=1; j<=(nlstate+ndeath);j++){  
             k=k+1;            k=k+1;
             mu[k][(int) age]=pmmij[i][j];            if (j >= jmax) {
           }              jmax=j;
         }              ijmax=i;
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)            }
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)            else if (j <= jmin){
             varpij[i][j][(int)age] = doldm[i][j];              jmin=j;
               ijmin=i;
         /*printf("\n%d ",(int)age);            }
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            if(j<0){
      }*/              nberr++;
               printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         fprintf(ficresprob,"\n%d ",(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]);
         fprintf(ficresprobcov,"\n%d ",(int)age);            }
         fprintf(ficresprobcor,"\n%d ",(int)age);            sum=sum+j;
           }
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)          jk= j/stepm;
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));          jl= j -jk*stepm;
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){          ju= j -(jk+1)*stepm;
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);            if(jl==0){
         }              dh[mi][i]=jk;
         i=0;              bh[mi][i]=0;
         for (k=1; k<=(nlstate);k++){            }else{ /* We want a negative bias in order to only have interpolation ie
           for (l=1; l<=(nlstate+ndeath);l++){                    * at the price of an extra matrix product in likelihood */
             i=i++;              dh[mi][i]=jk+1;
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);              bh[mi][i]=ju;
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);            }
             for (j=1; j<=i;j++){          }else{
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);            if(jl <= -ju){
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));              dh[mi][i]=jk;
             }              bh[mi][i]=jl;       /* bias is positive if real duration
           }                                   * is higher than the multiple of stepm and negative otherwise.
         }/* end of loop for state */                                   */
       } /* end of loop for age */            }
             else{
       /* Confidence intervalle of pij  */              dh[mi][i]=jk+1;
       /*              bh[mi][i]=ju;
       fprintf(ficgp,"\nset noparametric;unset label");            }
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");            if(dh[mi][i]==0){
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");              dh[mi][i]=1; /* At least one step */
       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);              bh[mi][i]=ju; /* At least one step */
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);              /*  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);*/
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);            }
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);          } /* end if mle */
       */        }
       } /* end wave */
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/    }
       first1=1;    jmean=sum/k;
       for (k1=1; k1<=(nlstate);k1++){    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
         for (l1=1; l1<=(nlstate+ndeath);l1++){    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
           if(l1==k1) continue;   }
           i=(k1-1)*(nlstate+ndeath)+l1;  
           for (k2=1; k2<=(nlstate);k2++){  /*********** Tricode ****************************/
             for (l2=1; l2<=(nlstate+ndeath);l2++){  void tricode(int *Tvar, int **nbcode, int imx)
               if(l2==k2) continue;  {
               j=(k2-1)*(nlstate+ndeath)+l2;    
               if(j<=i) continue;    int Ndum[20],ij=1, k, j, i, maxncov=19;
               for (age=bage; age<=fage; age ++){    int cptcode=0;
                 if ((int)age %5==0){    cptcoveff=0; 
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;   
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;    for (k=0; k<maxncov; k++) Ndum[k]=0;
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;    for (k=1; k<=7; k++) ncodemax[k]=0;
                   mu1=mu[i][(int) age]/stepm*YEARM ;  
                   mu2=mu[j][(int) age]/stepm*YEARM;    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
                   /* Computing eigen value of matrix of covariance */      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));                                 modality*/ 
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
                   if(first1==1){        Ndum[ij]++; /*store the modality */
                     first1=0;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
                     printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\nOthers in log...\n",v1,v2,cv12,lc1,lc2);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                   }                                         Tvar[j]. If V=sex and male is 0 and 
                   fprintf(ficlog,"Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);                                         female is 1, then  cptcode=1.*/
                   /* Eigen vectors */      }
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));  
                   v21=sqrt(1.-v11*v11);      for (i=0; i<=cptcode; i++) {
                   v12=-v21;        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 */
                   v22=v11;      }
                   /*printf(fignu*/  
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */      ij=1; 
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */      for (i=1; i<=ncodemax[j]; i++) {
                   if(first==1){        for (k=0; k<= maxncov; k++) {
                     first=0;          if (Ndum[k] != 0) {
                     fprintf(ficgp,"\nset parametric;set nolabel");            nbcode[Tvar[j]][ij]=k; 
                     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);            /* 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; */
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");            
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);            ij++;
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);          }
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);          if (ij > ncodemax[j]) break; 
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);        }  
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);      } 
                     /*              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\"",\    }  
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \  
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);   for (k=0; k< maxncov; k++) Ndum[k]=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)) not",\   for (i=1; i<=ncovmodel-2; i++) { 
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));     ij=Tvar[i];
                   }else{     Ndum[ij]++;
                     first=0;   }
                     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);   ij=1;
                     /*   for (i=1; i<= maxncov; i++) {
                     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\"",\     if((Ndum[i]!=0) && (i<=ncovcol)){
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \       Tvaraff[ij]=i; /*For printing */
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);       ij++;
                     */     }
                     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",\   }
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \   
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));   cptcoveff=ij-1; /*Number of simple covariates*/
                   }/* if first */  }
                 } /* age mod 5 */  
               } /* end loop age */  /*********** Health Expectancies ****************/
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);  
               first=1;  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
             } /*l12 */  
           } /* k12 */  {
         } /*l1 */    /* Health expectancies, no variances */
       }/* k1 */    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
     } /* loop covariates */    double age, agelim, hf;
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);    double ***p3mat;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    double eip;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);    pstamp(ficreseij);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    fprintf(ficreseij,"# Age");
   }    for(i=1; i<=nlstate;i++){
   free_vector(xp,1,npar);      for(j=1; j<=nlstate;j++){
   fclose(ficresprob);        fprintf(ficreseij," e%1d%1d ",i,j);
   fclose(ficresprobcov);      }
   fclose(ficresprobcor);      fprintf(ficreseij," e%1d. ",i);
   fclose(ficgp);    }
   fclose(fichtm);    fprintf(ficreseij,"\n");
 }  
     
     if(estepm < stepm){
 /******************* Printing html file ***********/      printf ("Problem %d lower than %d\n",estepm, stepm);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    }
                   int lastpass, int stepm, int weightopt, char model[],\    else  hstepm=estepm;   
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\    /* We compute the life expectancy from trapezoids spaced every estepm months
                   int popforecast, int estepm ,\     * This is mainly to measure the difference between two models: for example
                   double jprev1, double mprev1,double anprev1, \     * if stepm=24 months pijx are given only every 2 years and by summing them
                   double jprev2, double mprev2,double anprev2){     * we are calculating an estimate of the Life Expectancy assuming a linear 
   int jj1, k1, i1, cpt;     * progression in between and thus overestimating or underestimating according
   /*char optionfilehtm[FILENAMELENGTH];*/     * to the curvature of the survival function. If, for the same date, we 
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     printf("Problem with %s \n",optionfilehtm), exit(0);     * to compare the new estimate of Life expectancy with the same linear 
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);     * hypothesis. A more precise result, taking into account a more precise
   }     * curvature will be obtained if estepm is as small as stepm. */
   
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n    /* For example we decided to compute the life expectancy with the smallest unit */
  - 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    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n       nhstepm is the number of hstepm from age to agelim 
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n       nstepm is the number of stepm from age to agelin. 
  - Life expectancies by age and initial health status (estepm=%2d months):       Look at hpijx to understand the reason of that which relies in memory size
    <a href=\"e%s\">e%s</a> <br>\n</li>", \       and note for a fixed period like estepm months */
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    /* 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(fichtm," \n<ul><li><b>Graphs</b></li><p>");       means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
  m=cptcoveff;       results. So we changed our mind and took the option of the best precision.
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
  jj1=0;  
  for(k1=1; k1<=m;k1++){    agelim=AGESUP;
    for(i1=1; i1<=ncodemax[k1];i1++){    /* nhstepm age range expressed in number of stepm */
      jj1++;    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
      if (cptcovn > 0) {    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    /* if (stepm >= YEARM) hstepm=1;*/
        for (cpt=1; cpt<=cptcoveff;cpt++)    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  
      }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
      /* Pij */      /* Computed by stepm unit matrices, product of hstepm matrices, stored
      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>         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          
      /* Quasi-incidences */      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>      
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
        /* Stable prevalence in each health state */      
        for(cpt=1; cpt<nlstate;cpt++){      printf("%d|",(int)age);fflush(stdout);
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      
        }      /* Computing expectancies */
      for(cpt=1; cpt<=nlstate;cpt++) {      for(i=1; i<=nlstate;i++)
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>        for(j=1; j<=nlstate;j++)
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          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;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            
 health expectancies in states (1) and (2): e%s%d.png<br>            /* 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]);*/
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  
    } /* end i1 */          }
  }/* End k1 */  
  fprintf(fichtm,"</ul>");      fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0;
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n        for(j=1; j<=nlstate;j++){
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n          eip +=eij[i][j][(int)age];
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n        }
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n        fprintf(ficreseij,"%9.4f", eip );
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n      }
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n      fprintf(ficreseij,"\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);      
     }
  if(popforecast==1) fprintf(fichtm,"\n    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    printf("\n");
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    fprintf(ficlog,"\n");
         <br>",fileres,fileres,fileres,fileres);    
  else  }
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);  
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");  void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
   
  m=cptcoveff;  {
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .
  jj1=0;    */
  for(k1=1; k1<=m;k1++){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
    for(i1=1; i1<=ncodemax[k1];i1++){    double age, agelim, hf;
      jj1++;    double ***p3matp, ***p3matm, ***varhe;
      if (cptcovn > 0) {    double **dnewm,**doldm;
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    double *xp, *xm;
        for (cpt=1; cpt<=cptcoveff;cpt++)    double **gp, **gm;
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    double ***gradg, ***trgradg;
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    int theta;
      }  
      for(cpt=1; cpt<=nlstate;cpt++) {    double eip, vip;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  
 interval) in state (%d): v%s%d%d.png <br>    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      xp=vector(1,npar);
      }    xm=vector(1,npar);
    } /* end i1 */    dnewm=matrix(1,nlstate*nlstate,1,npar);
  }/* End k1 */    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
  fprintf(fichtm,"</ul>");    
 fclose(fichtm);    pstamp(ficresstdeij);
 }    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
 /******************* Gnuplot file **************/    for(i=1; i<=nlstate;i++){
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){      for(j=1; j<=nlstate;j++)
         fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      fprintf(ficresstdeij," e%1d. ",i);
   int ng;    }
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    fprintf(ficresstdeij,"\n");
     printf("Problem with file %s",optionfilegnuplot);  
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);    pstamp(ficrescveij);
   }    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
     fprintf(ficrescveij,"# Age");
 #ifdef windows    for(i=1; i<=nlstate;i++)
     fprintf(ficgp,"cd \"%s\" \n",pathc);      for(j=1; j<=nlstate;j++){
 #endif        cptj= (j-1)*nlstate+i;
 m=pow(2,cptcoveff);        for(i2=1; i2<=nlstate;i2++)
            for(j2=1; j2<=nlstate;j2++){
  /* 1eme*/            cptj2= (j2-1)*nlstate+i2;
   for (cpt=1; cpt<= nlstate ; cpt ++) {            if(cptj2 <= cptj)
    for (k1=1; k1<= m ; k1 ++) {              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           }
 #ifdef windows      }
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    fprintf(ficrescveij,"\n");
      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);    
 #endif    if(estepm < stepm){
 #ifdef unix      printf ("Problem %d lower than %d\n",estepm, stepm);
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    }
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    else  hstepm=estepm;   
 #endif    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
 for (i=1; i<= nlstate ; i ++) {     * if stepm=24 months pijx are given only every 2 years and by summing them
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");     * we are calculating an estimate of the Life Expectancy assuming a linear 
   else fprintf(ficgp," \%%*lf (\%%*lf)");     * progression in between and thus overestimating or underestimating according
 }     * to the curvature of the survival function. If, for the same date, we 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     for (i=1; i<= nlstate ; i ++) {     * to compare the new estimate of Life expectancy with the same linear 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");     * hypothesis. A more precise result, taking into account a more precise
   else fprintf(ficgp," \%%*lf (\%%*lf)");     * curvature will be obtained if estepm is as small as stepm. */
 }  
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    /* For example we decided to compute the life expectancy with the smallest unit */
      for (i=1; i<= nlstate ; i ++) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");       nhstepm is the number of hstepm from age to agelim 
   else fprintf(ficgp," \%%*lf (\%%*lf)");       nstepm is the number of stepm from age to agelin. 
 }         Look at hpijx to understand the reason of that which relies in memory size
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));       and note for a fixed period like estepm months */
 #ifdef unix    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");       survival function given by stepm (the optimization length). Unfortunately it
 #endif       means that if the survival funtion is printed only each two years of age and if
    }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   }       results. So we changed our mind and took the option of the best precision.
   /*2 eme*/    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   for (k1=1; k1<= m ; k1 ++) {  
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);    /* If stepm=6 months */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);    /* nhstepm age range expressed in number of stepm */
        agelim=AGESUP;
     for (i=1; i<= nlstate+1 ; i ++) {    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       k=2*i;    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    /* if (stepm >= YEARM) hstepm=1;*/
       for (j=1; j<= nlstate+1 ; j ++) {    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    
   else fprintf(ficgp," \%%*lf (\%%*lf)");    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 }      p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    gp=matrix(0,nhstepm,1,nlstate*nlstate);
       for (j=1; j<= nlstate+1 ; j ++) {    gm=matrix(0,nhstepm,1,nlstate*nlstate);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
         else fprintf(ficgp," \%%*lf (\%%*lf)");    for (age=bage; age<=fage; age ++){ 
 }    
       fprintf(ficgp,"\" t\"\" w l 0,");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       for (j=1; j<= nlstate+1 ; j ++) {   
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }        /* Computing  Variances of health expectancies */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
       else fprintf(ficgp,"\" t\"\" w l 0,");         decrease memory allocation */
     }      for(theta=1; theta <=npar; theta++){
   }        for(i=1; i<=npar; i++){ 
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
   /*3eme*/          xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }
   for (k1=1; k1<= m ; k1 ++) {        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
     for (cpt=1; cpt<= nlstate ; cpt ++) {        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
       k=2+nlstate*(2*cpt-2);    
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        for(j=1; j<= nlstate; j++){
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);          for(i=1; i<=nlstate; i++){
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);            for(h=0; h<=nhstepm-1; h++){
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);            }
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          }
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        }
        
 */        for(ij=1; ij<= nlstate*nlstate; ij++)
       for (i=1; i< nlstate ; i ++) {          for(h=0; h<=nhstepm-1; h++){
         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);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
       }      }/* End theta */
     }      
   }      
        for(h=0; h<=nhstepm-1; h++)
   /* CV preval stat */        for(j=1; j<=nlstate*nlstate;j++)
     for (k1=1; k1<= m ; k1 ++) {          for(theta=1; theta <=npar; theta++)
     for (cpt=1; cpt<nlstate ; cpt ++) {            trgradg[h][j][theta]=gradg[h][theta][j];
       k=3;      
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);       for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
       for (i=1; i< nlstate ; i ++)          varhe[ij][ji][(int)age] =0.;
         fprintf(ficgp,"+$%d",k+i+1);  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);       printf("%d|",(int)age);fflush(stdout);
             fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       l=3+(nlstate+ndeath)*cpt;       for(h=0;h<=nhstepm-1;h++){
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        for(k=0;k<=nhstepm-1;k++){
       for (i=1; i< nlstate ; i ++) {          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
         l=3+(nlstate+ndeath)*cpt;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
         fprintf(ficgp,"+$%d",l+i+1);          for(ij=1;ij<=nlstate*nlstate;ij++)
       }            for(ji=1;ji<=nlstate*nlstate;ji++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     }        }
   }        }
        /* Computing expectancies */
   /* proba elementaires */      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
    for(i=1,jk=1; i <=nlstate; i++){      for(i=1; i<=nlstate;i++)
     for(k=1; k <=(nlstate+ndeath); k++){        for(j=1; j<=nlstate;j++)
       if (k != i) {          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
         for(j=1; j <=ncovmodel; j++){            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            
           jk++;            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
           fprintf(ficgp,"\n");  
         }          }
       }  
     }      fprintf(ficresstdeij,"%3.0f",age );
    }      for(i=1; i<=nlstate;i++){
         eip=0.;
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/        vip=0.;
      for(jk=1; jk <=m; jk++) {        for(j=1; j<=nlstate;j++){
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);          eip += eij[i][j][(int)age];
        if (ng==2)          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
        else          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
          fprintf(ficgp,"\nset title \"Probability\"\n");        }
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
        i=1;      }
        for(k2=1; k2<=nlstate; k2++) {      fprintf(ficresstdeij,"\n");
          k3=i;  
          for(k=1; k<=(nlstate+ndeath); k++) {      fprintf(ficrescveij,"%3.0f",age );
            if (k != k2){      for(i=1; i<=nlstate;i++)
              if(ng==2)        for(j=1; j<=nlstate;j++){
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);          cptj= (j-1)*nlstate+i;
              else          for(i2=1; i2<=nlstate;i2++)
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            for(j2=1; j2<=nlstate;j2++){
              ij=1;              cptj2= (j2-1)*nlstate+i2;
              for(j=3; j <=ncovmodel; j++) {              if(cptj2 <= cptj)
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            }
                  ij++;        }
                }      fprintf(ficrescveij,"\n");
                else     
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    }
              }    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
              fprintf(ficgp,")/(1");    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
                  free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
              for(k1=1; k1 <=nlstate; k1++){      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                ij=1;    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                for(j=3; j <=ncovmodel; j++){    printf("\n");
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    fprintf(ficlog,"\n");
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
                    ij++;    free_vector(xm,1,npar);
                  }    free_vector(xp,1,npar);
                  else    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
                }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
                fprintf(ficgp,")");  }
              }  
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);  /************ Variance ******************/
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");  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, char strstart[])
              i=i+ncovmodel;  {
            }    /* Variance of health expectancies */
          } /* end k */    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
        } /* end k2 */    /* double **newm;*/
      } /* end jk */    double **dnewm,**doldm;
    } /* end ng */    double **dnewmp,**doldmp;
    fclose(ficgp);    int i, j, nhstepm, hstepm, h, nstepm ;
 }  /* end gnuplot */    int k, cptcode;
     double *xp;
     double **gp, **gm;  /* for var eij */
 /*************** Moving average **************/    double ***gradg, ***trgradg; /*for var eij */
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
   int i, cpt, cptcod;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    double ***p3mat;
       for (i=1; i<=nlstate;i++)    double age,agelim, hf;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    double ***mobaverage;
           mobaverage[(int)agedeb][i][cptcod]=0.;    int theta;
        char digit[4];
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    char digitp[25];
       for (i=1; i<=nlstate;i++){  
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    char fileresprobmorprev[FILENAMELENGTH];
           for (cpt=0;cpt<=4;cpt++){  
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    if(popbased==1){
           }      if(mobilav!=0)
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        strcpy(digitp,"-populbased-mobilav-");
         }      else strcpy(digitp,"-populbased-nomobil-");
       }    }
     }    else 
          strcpy(digitp,"-stablbased-");
 }  
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 /************** Forecasting ******************/      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
 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," Error in movingaverage mobilav=%d\n",mobilav);
          printf(" Error in movingaverage mobilav=%d\n",mobilav);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      }
   int *popage;    }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;    strcpy(fileresprobmorprev,"prmorprev"); 
   double ***p3mat;    sprintf(digit,"%-d",ij);
   char fileresf[FILENAMELENGTH];    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
  agelim=AGESUP;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
      }
   strcpy(fileresf,"f");    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   strcat(fileresf,fileres);   
   if((ficresf=fopen(fileresf,"w"))==NULL) {    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     printf("Problem with forecast resultfile: %s\n", fileresf);    pstamp(ficresprobmorprev);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);    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);
   }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   printf("Computing forecasting: result on file '%s' \n", fileresf);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);      fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
   if (mobilav==1) {    fprintf(ficresprobmorprev,"\n");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficgp,"\n# Routine varevsij");
     movingaverage(agedeb, fage, ageminpar, mobaverage);    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   }    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);
   stepsize=(int) (stepm+YEARM-1)/YEARM;  /*   } */
   if (stepm<=12) stepsize=1;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      pstamp(ficresvij);
   agelim=AGESUP;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
      if(popbased==1)
   hstepm=1;      fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
   hstepm=hstepm/stepm;    else
   yp1=modf(dateintmean,&yp);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   anprojmean=yp;    fprintf(ficresvij,"# Age");
   yp2=modf((yp1*12),&yp);    for(i=1; i<=nlstate;i++)
   mprojmean=yp;      for(j=1; j<=nlstate;j++)
   yp1=modf((yp2*30.5),&yp);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
   jprojmean=yp;    fprintf(ficresvij,"\n");
   if(jprojmean==0) jprojmean=1;  
   if(mprojmean==0) jprojmean=1;    xp=vector(1,npar);
      dnewm=matrix(1,nlstate,1,npar);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    doldm=matrix(1,nlstate,1,nlstate);
      dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   for(cptcov=1;cptcov<=i2;cptcov++){    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       fprintf(ficresf,"\n#******");    gpp=vector(nlstate+1,nlstate+ndeath);
       for(j=1;j<=cptcoveff;j++) {    gmp=vector(nlstate+1,nlstate+ndeath);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       }    
       fprintf(ficresf,"******\n");    if(estepm < stepm){
       fprintf(ficresf,"# StartingAge FinalAge");      printf ("Problem %d lower than %d\n",estepm, stepm);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    }
          else  hstepm=estepm;   
          /* For example we decided to compute the life expectancy with the smallest unit */
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         fprintf(ficresf,"\n");       nhstepm is the number of hstepm from age to agelim 
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);         nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){       and note for a fixed period like k years */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           nhstepm = nhstepm/hstepm;       survival function given by stepm (the optimization length). Unfortunately it
                 means that if the survival funtion is printed every two years of age and if
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           oldm=oldms;savm=savms;       results. So we changed our mind and took the option of the best precision.
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      */
            hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           for (h=0; h<=nhstepm; h++){    agelim = AGESUP;
             if (h==(int) (calagedate+YEARM*cpt)) {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);      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 */
             for(j=1; j<=nlstate+ndeath;j++) {      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               kk1=0.;kk2=0;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
               for(i=1; i<=nlstate;i++) {                    gp=matrix(0,nhstepm,1,nlstate);
                 if (mobilav==1)      gm=matrix(0,nhstepm,1,nlstate);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      for(theta=1; theta <=npar; theta++){
                 }        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
                          xp[i] = x[i] + (i==theta ?delti[theta]:0);
               }        }
               if (h==(int)(calagedate+12*cpt)){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                 fprintf(ficresf," %.3f", kk1);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                          
               }        if (popbased==1) {
             }          if(mobilav ==0){
           }            for(i=1; i<=nlstate;i++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              prlim[i][i]=probs[(int)age][i][ij];
         }          }else{ /* mobilav */ 
       }            for(i=1; i<=nlstate;i++)
     }              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
                }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    
         for(j=1; j<= nlstate; j++){
   fclose(ficresf);          for(h=0; h<=nhstepm; h++){
 }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
 /************** Forecasting ******************/              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
 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;        /* This for computing probability of death (h=1 means
   int *popage;           computed over hstepm matrices product = hstepm*stepm months) 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;           as a weighted average of prlim.
   double *popeffectif,*popcount;        */
   double ***p3mat,***tabpop,***tabpopprev;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   char filerespop[FILENAMELENGTH];          for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }    
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        /* end probability of death */
   agelim=AGESUP;  
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     
   strcpy(filerespop,"pop");        if (popbased==1) {
   strcat(filerespop,fileres);          if(mobilav ==0){
   if((ficrespop=fopen(filerespop,"w"))==NULL) {            for(i=1; i<=nlstate;i++)
     printf("Problem with forecast resultfile: %s\n", filerespop);              prlim[i][i]=probs[(int)age][i][ij];
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);          }else{ /* mobilav */ 
   }            for(i=1; i<=nlstate;i++)
   printf("Computing forecasting: result on file '%s' \n", filerespop);              prlim[i][i]=mobaverage[(int)age][i][ij];
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);          }
         }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
         for(j=1; j<= nlstate; j++){
   if (mobilav==1) {          for(h=0; h<=nhstepm; h++){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     movingaverage(agedeb, fage, ageminpar, mobaverage);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   }          }
         }
   stepsize=(int) (stepm+YEARM-1)/YEARM;        /* This for computing probability of death (h=1 means
   if (stepm<=12) stepsize=1;           computed over hstepm matrices product = hstepm*stepm months) 
             as a weighted average of prlim.
   agelim=AGESUP;        */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
   hstepm=1;          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   hstepm=hstepm/stepm;           gmp[j] += prlim[i][i]*p3mat[i][j][1];
          }    
   if (popforecast==1) {        /* end probability of death */
     if((ficpop=fopen(popfile,"r"))==NULL) {  
       printf("Problem with population file : %s\n",popfile);exit(0);        for(j=1; j<= nlstate; j++) /* vareij */
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);          for(h=0; h<=nhstepm; h++){
     }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     popage=ivector(0,AGESUP);          }
     popeffectif=vector(0,AGESUP);  
     popcount=vector(0,AGESUP);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
              gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     i=1;          }
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;  
          } /* End theta */
     imx=i;  
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   }  
       for(h=0; h<=nhstepm; h++) /* veij */
   for(cptcov=1;cptcov<=i2;cptcov++){        for(j=1; j<=nlstate;j++)
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          for(theta=1; theta <=npar; theta++)
       k=k+1;            trgradg[h][j][theta]=gradg[h][theta][j];
       fprintf(ficrespop,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(theta=1; theta <=npar; theta++)
       }          trgradgp[j][theta]=gradgp[theta][j];
       fprintf(ficrespop,"******\n");    
       fprintf(ficrespop,"# Age");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       if (popforecast==1)  fprintf(ficrespop," [Population]");      for(i=1;i<=nlstate;i++)
              for(j=1;j<=nlstate;j++)
       for (cpt=0; cpt<=0;cpt++) {          vareij[i][j][(int)age] =0.;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    
              for(h=0;h<=nhstepm;h++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        for(k=0;k<=nhstepm;k++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           nhstepm = nhstepm/hstepm;          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
                    for(i=1;i<=nlstate;i++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(j=1;j<=nlstate;j++)
           oldm=oldms;savm=savms;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          }
              }
           for (h=0; h<=nhstepm; h++){    
             if (h==(int) (calagedate+YEARM*cpt)) {      /* pptj */
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
             }      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
             for(j=1; j<=nlstate+ndeath;j++) {      for(j=nlstate+1;j<=nlstate+ndeath;j++)
               kk1=0.;kk2=0;        for(i=nlstate+1;i<=nlstate+ndeath;i++)
               for(i=1; i<=nlstate;i++) {                        varppt[j][i]=doldmp[j][i];
                 if (mobilav==1)      /* end ppptj */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      /*  x centered again */
                 else {      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
                 }   
               }      if (popbased==1) {
               if (h==(int)(calagedate+12*cpt)){        if(mobilav ==0){
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          for(i=1; i<=nlstate;i++)
                   /*fprintf(ficrespop," %.3f", kk1);            prlim[i][i]=probs[(int)age][i][ij];
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        }else{ /* mobilav */ 
               }          for(i=1; i<=nlstate;i++)
             }            prlim[i][i]=mobaverage[(int)age][i][ij];
             for(i=1; i<=nlstate;i++){        }
               kk1=0.;      }
                 for(j=1; j<=nlstate;j++){               
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];      /* This for computing probability of death (h=1 means
                 }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];         as a weighted average of prlim.
             }      */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           }      }    
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* end probability of death */
         }  
       }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
        for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   /******/        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      } 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      fprintf(ficresprobmorprev,"\n");
           nhstepm = nhstepm/hstepm;  
                fprintf(ficresvij,"%.0f ",age );
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(i=1; i<=nlstate;i++)
           oldm=oldms;savm=savms;        for(j=1; j<=nlstate;j++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
           for (h=0; h<=nhstepm; h++){        }
             if (h==(int) (calagedate+YEARM*cpt)) {      fprintf(ficresvij,"\n");
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      free_matrix(gp,0,nhstepm,1,nlstate);
             }      free_matrix(gm,0,nhstepm,1,nlstate);
             for(j=1; j<=nlstate+ndeath;j++) {      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
               kk1=0.;kk2=0;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
               for(i=1; i<=nlstate;i++) {                    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        } /* End age */
               }    free_vector(gpp,nlstate+1,nlstate+ndeath);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    free_vector(gmp,nlstate+1,nlstate+ndeath);
             }    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
           }    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
         }    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       }    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
    }  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
   if (popforecast==1) {    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     free_ivector(popage,0,AGESUP);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     free_vector(popeffectif,0,AGESUP);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     free_vector(popcount,0,AGESUP);    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   }  */
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   fclose(ficrespop);  
 }    free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
 /***********************************************/    free_matrix(dnewm,1,nlstate,1,npar);
 /**************** Main Program *****************/    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);
 int main(int argc, char *argv[])    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 {    fclose(ficresprobmorprev);
     fflush(ficgp);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    fflush(fichtm); 
   double agedeb, agefin,hf;  }  /* end varevsij */
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;  
   /************ Variance of prevlim ******************/
   double fret;  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 strstart[])
   double **xi,tmp,delta;  {
     /* Variance of prevalence limit */
   double dum; /* Dummy variable */    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   double ***p3mat;    double **newm;
   int *indx;    double **dnewm,**doldm;
   char line[MAXLINE], linepar[MAXLINE];    int i, j, nhstepm, hstepm;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];    int k, cptcode;
   int firstobs=1, lastobs=10;    double *xp;
   int sdeb, sfin; /* Status at beginning and end */    double *gp, *gm;
   int c,  h , cpt,l;    double **gradg, **trgradg;
   int ju,jl, mi;    double age,agelim;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    int theta;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    
   int mobilav=0,popforecast=0;    pstamp(ficresvpl);
   int hstepm, nhstepm;    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
   double bage, fage, age, agelim, agebase;        fprintf(ficresvpl," %1d-%1d",i,i);
   double ftolpl=FTOL;    fprintf(ficresvpl,"\n");
   double **prlim;  
   double *severity;    xp=vector(1,npar);
   double ***param; /* Matrix of parameters */    dnewm=matrix(1,nlstate,1,npar);
   double  *p;    doldm=matrix(1,nlstate,1,nlstate);
   double **matcov; /* Matrix of covariance */    
   double ***delti3; /* Scale */    hstepm=1*YEARM; /* Every year of age */
   double *delti; /* Scale */    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   double ***eij, ***vareij;    agelim = AGESUP;
   double **varpl; /* Variances of prevalence limits by age */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   double *epj, vepp;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   double kk1, kk2;      if (stepm >= YEARM) hstepm=1;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
        gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
   char *alph[]={"a","a","b","c","d","e"}, str[4];      gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
   char z[1]="c", occ;        for(i=1; i<=npar; i++){ /* Computes gradient */
 #include <sys/time.h>          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 #include <time.h>        }
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
          for(i=1;i<=nlstate;i++)
   /* long total_usecs;          gp[i] = prlim[i][i];
   struct timeval start_time, end_time;      
          for(i=1; i<=npar; i++) /* Computes gradient */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   getcwd(pathcd, size);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
   printf("\n%s",version);          gm[i] = prlim[i][i];
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");        for(i=1;i<=nlstate;i++)
     scanf("%s",pathtot);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   }      } /* End theta */
   else{  
     strcpy(pathtot,argv[1]);      trgradg =matrix(1,nlstate,1,npar);
   }  
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/      for(j=1; j<=nlstate;j++)
   /*cygwin_split_path(pathtot,path,optionfile);        for(theta=1; theta <=npar; theta++)
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          trgradg[j][theta]=gradg[theta][j];
   /* cutv(path,optionfile,pathtot,'\\');*/  
       for(i=1;i<=nlstate;i++)
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        varpl[i][(int)age] =0.;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   chdir(path);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   replace(pathc,path);      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
 /*-------- arguments in the command line --------*/  
       fprintf(ficresvpl,"%.0f ",age );
   /* Log file */      for(i=1; i<=nlstate;i++)
   strcat(filelog, optionfilefiname);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   strcat(filelog,".log");    /* */      fprintf(ficresvpl,"\n");
   if((ficlog=fopen(filelog,"w"))==NULL)    {      free_vector(gp,1,nlstate);
     printf("Problem with logfile %s\n",filelog);      free_vector(gm,1,nlstate);
     goto end;      free_matrix(gradg,1,npar,1,nlstate);
   }      free_matrix(trgradg,1,nlstate,1,npar);
   fprintf(ficlog,"Log filename:%s\n",filelog);    } /* End age */
   fprintf(ficlog,"\n%s",version);  
   fprintf(ficlog,"\nEnter the parameter file name: ");    free_vector(xp,1,npar);
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    free_matrix(doldm,1,nlstate,1,npar);
   fflush(ficlog);    free_matrix(dnewm,1,nlstate,1,nlstate);
   
   /* */  }
   strcpy(fileres,"r");  
   strcat(fileres, optionfilefiname);  /************ Variance of one-step probabilities  ******************/
   strcat(fileres,".txt");    /* Other files have txt extension */  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
   /*---------arguments file --------*/    int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    int k=0,l, cptcode;
     printf("Problem with optionfile %s\n",optionfile);    int first=1, first1;
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     goto end;    double **dnewm,**doldm;
   }    double *xp;
     double *gp, *gm;
   strcpy(filereso,"o");    double **gradg, **trgradg;
   strcat(filereso,fileres);    double **mu;
   if((ficparo=fopen(filereso,"w"))==NULL) {    double age,agelim, cov[NCOVMAX];
     printf("Problem with Output resultfile: %s\n", filereso);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);    int theta;
     goto end;    char fileresprob[FILENAMELENGTH];
   }    char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    double ***varpij;
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    strcpy(fileresprob,"prob"); 
     puts(line);    strcat(fileresprob,fileres);
     fputs(line,ficparo);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprob);
   ungetc(c,ficpar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
   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);    strcpy(fileresprobcov,"probcov"); 
   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);    strcat(fileresprobcov,fileres);
   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);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
 while((c=getc(ficpar))=='#' && c!= EOF){      printf("Problem with resultfile: %s\n", fileresprobcov);
     ungetc(c,ficpar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    strcpy(fileresprobcor,"probcor"); 
     fputs(line,ficparo);    strcat(fileresprobcor,fileres);
   }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   ungetc(c,ficpar);      printf("Problem with resultfile: %s\n", fileresprobcor);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
        }
   covar=matrix(0,NCOVMAX,1,n);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   cptcovn=0;    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   ncovmodel=2+cptcovn;    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      pstamp(ficresprob);
   /* Read guess parameters */    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   /* Reads comments: lines beginning with '#' */    fprintf(ficresprob,"# Age");
   while((c=getc(ficpar))=='#' && c!= EOF){    pstamp(ficresprobcov);
     ungetc(c,ficpar);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fgets(line, MAXLINE, ficpar);    fprintf(ficresprobcov,"# Age");
     puts(line);    pstamp(ficresprobcor);
     fputs(line,ficparo);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   }    fprintf(ficresprobcor,"# Age");
   ungetc(c,ficpar);  
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    for(i=1; i<=nlstate;i++)
     for(i=1; i <=nlstate; i++)      for(j=1; j<=(nlstate+ndeath);j++){
     for(j=1; j <=nlstate+ndeath-1; j++){        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
       fscanf(ficpar,"%1d%1d",&i1,&j1);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
       fprintf(ficparo,"%1d%1d",i1,j1);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       if(mle==1)      }  
         printf("%1d%1d",i,j);   /* fprintf(ficresprob,"\n");
       fprintf(ficlog,"%1d%1d",i,j);    fprintf(ficresprobcov,"\n");
       for(k=1; k<=ncovmodel;k++){    fprintf(ficresprobcor,"\n");
         fscanf(ficpar," %lf",&param[i][j][k]);   */
         if(mle==1){   xp=vector(1,npar);
           printf(" %lf",param[i][j][k]);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           fprintf(ficlog," %lf",param[i][j][k]);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
         }    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
         else    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
           fprintf(ficlog," %lf",param[i][j][k]);    first=1;
         fprintf(ficparo," %lf",param[i][j][k]);    fprintf(ficgp,"\n# Routine varprob");
       }    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       fscanf(ficpar,"\n");    fprintf(fichtm,"\n");
       if(mle==1)  
         printf("\n");    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
       fprintf(ficlog,"\n");    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
       fprintf(ficparo,"\n");    file %s<br>\n",optionfilehtmcov);
     }    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
    and drawn. It helps understanding how is the covariance between two incidences.\
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   p=param[1][1];  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
    would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   /* Reads comments: lines beginning with '#' */  standard deviations wide on each axis. <br>\
   while((c=getc(ficpar))=='#' && c!= EOF){   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>\
     fgets(line, MAXLINE, ficpar);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
     puts(line);  
     fputs(line,ficparo);    cov[1]=1;
   }    tj=cptcoveff;
   ungetc(c,ficpar);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    for(t=1; t<=tj;t++){
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      for(i1=1; i1<=ncodemax[t];i1++){ 
   for(i=1; i <=nlstate; i++){        j1++;
     for(j=1; j <=nlstate+ndeath-1; j++){        if  (cptcovn>0) {
       fscanf(ficpar,"%1d%1d",&i1,&j1);          fprintf(ficresprob, "\n#********** Variable "); 
       printf("%1d%1d",i,j);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fprintf(ficparo,"%1d%1d",i1,j1);          fprintf(ficresprob, "**********\n#\n");
       for(k=1; k<=ncovmodel;k++){          fprintf(ficresprobcov, "\n#********** Variable "); 
         fscanf(ficpar,"%le",&delti3[i][j][k]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         printf(" %le",delti3[i][j][k]);          fprintf(ficresprobcov, "**********\n#\n");
         fprintf(ficparo," %le",delti3[i][j][k]);          
       }          fprintf(ficgp, "\n#********** Variable "); 
       fscanf(ficpar,"\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       printf("\n");          fprintf(ficgp, "**********\n#\n");
       fprintf(ficparo,"\n");          
     }          
   }          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   delti=delti3[1][1];          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   /* Reads comments: lines beginning with '#' */          
   while((c=getc(ficpar))=='#' && c!= EOF){          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]]);
     fgets(line, MAXLINE, ficpar);          fprintf(ficresprobcor, "**********\n#");    
     puts(line);        }
     fputs(line,ficparo);        
   }        for (age=bage; age<=fage; age ++){ 
   ungetc(c,ficpar);          cov[2]=age;
            for (k=1; k<=cptcovn;k++) {
   matcov=matrix(1,npar,1,npar);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   for(i=1; i <=npar; i++){          }
     fscanf(ficpar,"%s",&str);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     if(mle==1)          for (k=1; k<=cptcovprod;k++)
       printf("%s",str);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     fprintf(ficlog,"%s",str);          
     fprintf(ficparo,"%s",str);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     for(j=1; j <=i; j++){          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       fscanf(ficpar," %le",&matcov[i][j]);          gp=vector(1,(nlstate)*(nlstate+ndeath));
       if(mle==1){          gm=vector(1,(nlstate)*(nlstate+ndeath));
         printf(" %.5le",matcov[i][j]);      
         fprintf(ficlog," %.5le",matcov[i][j]);          for(theta=1; theta <=npar; theta++){
       }            for(i=1; i<=npar; i++)
       else              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
         fprintf(ficlog," %.5le",matcov[i][j]);            
       fprintf(ficparo," %.5le",matcov[i][j]);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     }            
     fscanf(ficpar,"\n");            k=0;
     if(mle==1)            for(i=1; i<= (nlstate); i++){
       printf("\n");              for(j=1; j<=(nlstate+ndeath);j++){
     fprintf(ficlog,"\n");                k=k+1;
     fprintf(ficparo,"\n");                gp[k]=pmmij[i][j];
   }              }
   for(i=1; i <=npar; i++)            }
     for(j=i+1;j<=npar;j++)            
       matcov[i][j]=matcov[j][i];            for(i=1; i<=npar; i++)
                  xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   if(mle==1)      
     printf("\n");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   fprintf(ficlog,"\n");            k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
     /*-------- Rewriting paramater file ----------*/                k=k+1;
      strcpy(rfileres,"r");    /* "Rparameterfile */                gm[k]=pmmij[i][j];
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/              }
      strcat(rfileres,".");    /* */            }
      strcat(rfileres,optionfilext);    /* Other files have txt extension */       
     if((ficres =fopen(rfileres,"w"))==NULL) {            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       printf("Problem writing new parameter file: %s\n", fileres);goto end;              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;          }
     }  
     fprintf(ficres,"#%s\n",version);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
                for(theta=1; theta <=npar; theta++)
     /*-------- data file ----------*/              trgradg[j][theta]=gradg[theta][j];
     if((fic=fopen(datafile,"r"))==NULL)    {          
       printf("Problem with datafile: %s\n", datafile);goto end;          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     }          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     n= lastobs;          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     severity = vector(1,maxwav);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     outcome=imatrix(1,maxwav+1,1,n);  
     num=ivector(1,n);          pmij(pmmij,cov,ncovmodel,x,nlstate);
     moisnais=vector(1,n);          
     annais=vector(1,n);          k=0;
     moisdc=vector(1,n);          for(i=1; i<=(nlstate); i++){
     andc=vector(1,n);            for(j=1; j<=(nlstate+ndeath);j++){
     agedc=vector(1,n);              k=k+1;
     cod=ivector(1,n);              mu[k][(int) age]=pmmij[i][j];
     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);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     anint=matrix(1,maxwav,1,n);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
     s=imatrix(1,maxwav+1,1,n);              varpij[i][j][(int)age] = doldm[i][j];
     adl=imatrix(1,maxwav+1,1,n);      
     tab=ivector(1,NCOVMAX);          /*printf("\n%d ",(int)age);
     ncodemax=ivector(1,8);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     i=1;            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     while (fgets(line, MAXLINE, fic) != NULL)    {            }*/
       if ((i >= firstobs) && (i <=lastobs)) {  
                  fprintf(ficresprob,"\n%d ",(int)age);
         for (j=maxwav;j>=1;j--){          fprintf(ficresprobcov,"\n%d ",(int)age);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          fprintf(ficresprobcor,"\n%d ",(int)age);
           strcpy(line,stra);  
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            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]);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          }
           i=0;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          for (k=1; k<=(nlstate);k++){
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);            for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
         for (j=ncovcol;j>=1;j--){              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);              for (j=1; j<=i;j++){
         }                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
         num[i]=atol(stra);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
                      }
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){            }
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/          }/* end of loop for state */
         } /* end of loop for age */
         i=i+1;  
       }        /* Confidence intervalle of pij  */
     }        /*
     /* printf("ii=%d", ij);          fprintf(ficgp,"\nset noparametric;unset label");
        scanf("%d",i);*/          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   imx=i-1; /* Number of individuals */          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
   /* for (i=1; i<=imx; i++){          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;        */
     }*/  
    /*  for (i=1; i<=imx; i++){        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
      if (s[4][i]==9)  s[4][i]=-1;        first1=1;
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/        for (k2=1; k2<=(nlstate);k2++){
            for (l2=1; l2<=(nlstate+ndeath);l2++){ 
              if(l2==k2) continue;
   /* Calculation of the number of parameter from char model*/            j=(k2-1)*(nlstate+ndeath)+l2;
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */            for (k1=1; k1<=(nlstate);k1++){
   Tprod=ivector(1,15);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   Tvaraff=ivector(1,15);                if(l1==k1) continue;
   Tvard=imatrix(1,15,1,2);                i=(k1-1)*(nlstate+ndeath)+l1;
   Tage=ivector(1,15);                      if(i<=j) continue;
                    for (age=bage; age<=fage; age ++){ 
   if (strlen(model) >1){                  if ((int)age %5==0){
     j=0, j1=0, k1=1, k2=1;                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     j=nbocc(model,'+');                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     j1=nbocc(model,'*');                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     cptcovn=j+1;                    mu1=mu[i][(int) age]/stepm*YEARM ;
     cptcovprod=j1;                    mu2=mu[j][(int) age]/stepm*YEARM;
                        c12=cv12/sqrt(v1*v2);
     strcpy(modelsav,model);                    /* Computing eigen value of matrix of covariance */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       printf("Error. Non available option model=%s ",model);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       fprintf(ficlog,"Error. Non available option model=%s ",model);                    /* Eigen vectors */
       goto end;                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     }                    /*v21=sqrt(1.-v11*v11); *//* error */
                        v21=(lc1-v1)/cv12*v11;
     for(i=(j+1); i>=1;i--){                    v12=-v21;
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */                    v22=v11;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */                    tnalp=v21/v11;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                    if(first1==1){
       /*scanf("%d",i);*/                      first1=0;
       if (strchr(strb,'*')) {  /* Model includes a product */                      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(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/                    }
         if (strcmp(strc,"age")==0) { /* Vn*age */                    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);
           cptcovprod--;                    /*printf(fignu*/
           cutv(strb,stre,strd,'V');                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
           cptcovage++;                    if(first==1){
             Tage[cptcovage]=i;                      first=0;
             /*printf("stre=%s ", stre);*/                      fprintf(ficgp,"\nset parametric;unset label");
         }                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
         else if (strcmp(strd,"age")==0) { /* or age*Vn */                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           cptcovprod--;                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
           cutv(strb,stre,strc,'V');   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
           Tvar[i]=atoi(stre);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
           cptcovage++;                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
           Tage[cptcovage]=i;                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
         }                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
         else {  /* Age is not in the model */                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           Tvar[i]=ncovcol+k1;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
           Tprod[k1]=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",\
           Tvard[k1][1]=atoi(strc); /* m*/                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
           Tvard[k1][2]=atoi(stre); /* n */                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
           Tvar[cptcovn+k2]=Tvard[k1][1];                    }else{
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                      first=0;
           for (k=1; k<=lastobs;k++)                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
           k1++;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
           k2=k2+2;                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
         }                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       else { /* no more sum */                    }/* if first */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/                  } /* age mod 5 */
        /*  scanf("%d",i);*/                } /* end loop age */
       cutv(strd,strc,strb,'V');                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
       Tvar[i]=atoi(strc);                first=1;
       }              } /*l12 */
       strcpy(modelsav,stra);              } /* k12 */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          } /*l1 */
         scanf("%d",i);*/        }/* k1 */
     } /* end of loop + */      } /* loop covariates */
   } /* end model */    }
      free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   printf("cptcovprod=%d ", cptcovprod);    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
   scanf("%d ",i);*/    free_vector(xp,1,npar);
     fclose(fic);    fclose(ficresprob);
     fclose(ficresprobcov);
     /*  if(mle==1){*/    fclose(ficresprobcor);
     if (weightopt != 1) { /* Maximisation without weights*/    fflush(ficgp);
       for(i=1;i<=n;i++) weight[i]=1.0;    fflush(fichtmcov);
     }  }
     /*-calculation of age at interview from date of interview and age at death -*/  
     agev=matrix(1,maxwav,1,imx);  
   /******************* Printing html file ***********/
     for (i=1; i<=imx; i++) {  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
       for(m=2; (m<= maxwav); m++) {                    int lastpass, int stepm, int weightopt, char model[],\
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
          anint[m][i]=9999;                    int popforecast, int estepm ,\
          s[m][i]=-1;                    double jprev1, double mprev1,double anprev1, \
        }                    double jprev2, double mprev2,double anprev2){
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    int jj1, k1, i1, cpt;
       }  
     }     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
     for (i=1; i<=imx; i++)  {  </ul>");
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
       for(m=1; (m<= maxwav); m++){   - 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(s[m][i] >0){             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
           if (s[m][i] >= nlstate+1) {     fprintf(fichtm,"\
             if(agedc[i]>0)   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
               if(moisdc[i]!=99 && andc[i]!=9999)             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
                 agev[m][i]=agedc[i];     fprintf(fichtm,"\
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
            else {             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
               if (andc[i]!=9999){     fprintf(fichtm,"\
               printf("Warning negative age at death: %d line:%d\n",num[i],i);   - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);     <a href=\"%s\">%s</a> <br>\n</li>",
               agev[m][i]=-1;             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
               }  
             }  
           }  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
           else if(s[m][i] !=9){ /* Should no more exist */  
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);   m=cptcoveff;
             if(mint[m][i]==99 || anint[m][i]==9999)   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
               agev[m][i]=1;  
             else if(agev[m][i] <agemin){   jj1=0;
               agemin=agev[m][i];   for(k1=1; k1<=m;k1++){
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/     for(i1=1; i1<=ncodemax[k1];i1++){
             }       jj1++;
             else if(agev[m][i] >agemax){       if (cptcovn > 0) {
               agemax=agev[m][i];         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/         for (cpt=1; cpt<=cptcoveff;cpt++) 
             }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
             /*agev[m][i]=anint[m][i]-annais[i];*/         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
             /*   agev[m][i] = age[i]+2*m;*/       }
           }       /* Pij */
           else { /* =9 */       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
             agev[m][i]=1;  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
             s[m][i]=-1;       /* 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: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
         else /*= 0 Unknown */  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
           agev[m][i]=1;         /* Period (stable) prevalence in each health state */
       }         for(cpt=1; cpt<nlstate;cpt++){
               fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
     }  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
     for (i=1; i<=imx; i++)  {         }
       for(m=1; (m<= maxwav); m++){       for(cpt=1; cpt<=nlstate;cpt++) {
         if (s[m][i] > (nlstate+ndeath)) {          fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
           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);    <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
           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;     } /* end i1 */
         }   }/* End k1 */
       }   fprintf(fichtm,"</ul>");
     }  
   
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);   fprintf(fichtm,"\
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
     free_vector(severity,1,maxwav);  
     free_imatrix(outcome,1,maxwav+1,1,n);   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
     free_vector(moisnais,1,n);           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
     free_vector(annais,1,n);   fprintf(fichtm,"\
     /* free_matrix(mint,1,maxwav,1,n);   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
        free_matrix(anint,1,maxwav,1,n);*/           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
     free_vector(moisdc,1,n);  
     free_vector(andc,1,n);   fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
               subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
     wav=ivector(1,imx);   fprintf(fichtm,"\
     dh=imatrix(1,lastpass-firstpass+1,1,imx);   - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
     mw=imatrix(1,lastpass-firstpass+1,1,imx);     <a href=\"%s\">%s</a> <br>\n</li>",
                 estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
     /* Concatenates waves */   fprintf(fichtm,"\
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);   - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
       Tcode=ivector(1,100);   fprintf(fichtm,"\
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);   - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
       ncodemax[1]=1;           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);   fprintf(fichtm,"\
         - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
    codtab=imatrix(1,100,1,10);           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    h=0;   fprintf(fichtm,"\
    m=pow(2,cptcoveff);   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
             subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){  /*  if(popforecast==1) fprintf(fichtm,"\n */
        for(j=1; j <= ncodemax[k]; j++){  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
            h++;  /*      <br>",fileres,fileres,fileres,fileres); */
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;  /*  else  */
            /*  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,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
          }   fflush(fichtm);
        }   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
      }  
    }   m=cptcoveff;
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       codtab[1][2]=1;codtab[2][2]=2; */  
    /* for(i=1; i <=m ;i++){   jj1=0;
       for(k=1; k <=cptcovn; k++){   for(k1=1; k1<=m;k1++){
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);     for(i1=1; i1<=ncodemax[k1];i1++){
       }       jj1++;
       printf("\n");       if (cptcovn > 0) {
       }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       scanf("%d",i);*/         for (cpt=1; cpt<=cptcoveff;cpt++) 
               fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
    /* Calculates basic frequencies. Computes observed prevalence at single age         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        and prints on file fileres'p'. */       }
        for(cpt=1; cpt<=nlstate;cpt++) {
             fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
      prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       }
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  health expectancies in states (1) and (2): %s%d.png<br>\
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
           } /* end i1 */
     /* For Powell, parameters are in a vector p[] starting at p[1]   }/* End k1 */
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */   fprintf(fichtm,"</ul>");
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */   fflush(fichtm);
   }
     if(mle==1){  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  /******************* Gnuplot file **************/
     }  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
      
     /*--------- results files --------------*/    char dirfileres[132],optfileres[132];
     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);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
      int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
    jk=1;  /*     printf("Problem with file %s",optionfilegnuplot); */
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
    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++){    /*#ifdef windows */
      for(k=1; k <=(nlstate+ndeath); k++){    fprintf(ficgp,"cd \"%s\" \n",pathc);
        if (k != i)      /*#endif */
          {    m=pow(2,cptcoveff);
            printf("%d%d ",i,k);  
            fprintf(ficlog,"%d%d ",i,k);    strcpy(dirfileres,optionfilefiname);
            fprintf(ficres,"%1d%1d ",i,k);    strcpy(optfileres,"vpl");
            for(j=1; j <=ncovmodel; j++){   /* 1eme*/
              printf("%f ",p[jk]);    for (cpt=1; cpt<= nlstate ; cpt ++) {
              fprintf(ficlog,"%f ",p[jk]);     for (k1=1; k1<= m ; k1 ++) {
              fprintf(ficres,"%f ",p[jk]);       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
              jk++;       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
            }       fprintf(ficgp,"set xlabel \"Age\" \n\
            printf("\n");  set ylabel \"Probability\" \n\
            fprintf(ficlog,"\n");  set ter png small\n\
            fprintf(ficres,"\n");  set size 0.65,0.65\n\
          }  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
      }  
    }       for (i=1; i<= nlstate ; i ++) {
    if(mle==1){         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
      /* Computing hessian and covariance matrix */         else fprintf(ficgp," \%%*lf (\%%*lf)");
      ftolhess=ftol; /* Usually correct */       }
      hesscov(matcov, p, npar, delti, ftolhess, func);       fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
    }       for (i=1; i<= nlstate ; i ++) {
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
    printf("# Scales (for hessian or gradient estimation)\n");         else fprintf(ficgp," \%%*lf (\%%*lf)");
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");       } 
    for(i=1,jk=1; i <=nlstate; i++){       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
      for(j=1; j <=nlstate+ndeath; j++){       for (i=1; i<= nlstate ; i ++) {
        if (j!=i) {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          fprintf(ficres,"%1d%1d",i,j);         else fprintf(ficgp," \%%*lf (\%%*lf)");
          printf("%1d%1d",i,j);       }  
          fprintf(ficlog,"%1d%1d",i,j);       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
          for(k=1; k<=ncovmodel;k++){     }
            printf(" %.5e",delti[jk]);    }
            fprintf(ficlog," %.5e",delti[jk]);    /*2 eme*/
            fprintf(ficres," %.5e",delti[jk]);    
            jk++;    for (k1=1; k1<= m ; k1 ++) { 
          }      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
          printf("\n");      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
          fprintf(ficlog,"\n");      
          fprintf(ficres,"\n");      for (i=1; i<= nlstate+1 ; i ++) {
        }        k=2*i;
      }        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
    }        for (j=1; j<= nlstate+1 ; j ++) {
              if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
    k=1;          else 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");        }   
    if(mle==1)        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
      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");        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
    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");        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
    for(i=1;i<=npar;i++){        for (j=1; j<= nlstate+1 ; j ++) {
      /*  if (k>nlstate) k=1;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
          i1=(i-1)/(ncovmodel*nlstate)+1;          else fprintf(ficgp," \%%*lf (\%%*lf)");
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        }   
          printf("%s%d%d",alph[k],i1,tab[i]);*/        fprintf(ficgp,"\" t\"\" w l 0,");
      fprintf(ficres,"%3d",i);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
      if(mle==1)        for (j=1; j<= nlstate+1 ; j ++) {
        printf("%3d",i);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
      fprintf(ficlog,"%3d",i);          else fprintf(ficgp," \%%*lf (\%%*lf)");
      for(j=1; j<=i;j++){        }   
        fprintf(ficres," %.5e",matcov[i][j]);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
        if(mle==1)        else fprintf(ficgp,"\" t\"\" w l 0,");
          printf(" %.5e",matcov[i][j]);      }
        fprintf(ficlog," %.5e",matcov[i][j]);    }
      }    
      fprintf(ficres,"\n");    /*3eme*/
      if(mle==1)    
        printf("\n");    for (k1=1; k1<= m ; k1 ++) { 
      fprintf(ficlog,"\n");      for (cpt=1; cpt<= nlstate ; cpt ++) {
      k++;        /*       k=2+nlstate*(2*cpt-2); */
    }        k=2+(nlstate+1)*(cpt-1);
            fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
    while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficgp,"set ter png small\n\
      ungetc(c,ficpar);  set size 0.65,0.65\n\
      fgets(line, MAXLINE, ficpar);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
      puts(line);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
      fputs(line,ficparo);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
    }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
    ungetc(c,ficpar);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
    estepm=0;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
    if (estepm==0 || estepm < stepm) estepm=stepm;          
    if (fage <= 2) {        */
      bage = ageminpar;        for (i=1; i< nlstate ; i ++) {
      fage = agemaxpar;          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
    }          /*      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);*/
              
    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(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
    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);    /* CV preval stable (period) */
      fgets(line, MAXLINE, ficpar);    for (k1=1; k1<= m ; k1 ++) { 
      puts(line);      for (cpt=1; cpt<=nlstate ; cpt ++) {
      fputs(line,ficparo);        k=3;
    }        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
    ungetc(c,ficpar);        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
    set ter png small\nset size 0.65,0.65\n\
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);  unset log y\n\
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        
            for (i=1; i< nlstate ; i ++)
    while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficgp,"+$%d",k+i+1);
      ungetc(c,ficpar);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
      fgets(line, MAXLINE, ficpar);        
      puts(line);        l=3+(nlstate+ndeath)*cpt;
      fputs(line,ficparo);        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
    }        for (i=1; i< nlstate ; i ++) {
    ungetc(c,ficpar);          l=3+(nlstate+ndeath)*cpt;
            fprintf(ficgp,"+$%d",l+i+1);
         }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      } 
     }  
   fscanf(ficpar,"pop_based=%d\n",&popbased);    
   fprintf(ficparo,"pop_based=%d\n",popbased);      /* proba elementaires */
   fprintf(ficres,"pop_based=%d\n",popbased);      for(i=1,jk=1; i <=nlstate; i++){
        for(k=1; k <=(nlstate+ndeath); k++){
   while((c=getc(ficpar))=='#' && c!= EOF){        if (k != i) {
     ungetc(c,ficpar);          for(j=1; j <=ncovmodel; j++){
     fgets(line, MAXLINE, ficpar);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
     puts(line);            jk++; 
     fputs(line,ficparo);            fprintf(ficgp,"\n");
   }          }
   ungetc(c,ficpar);        }
       }
   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);  
 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);     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
 while((c=getc(ficpar))=='#' && c!= EOF){         if (ng==2)
     ungetc(c,ficpar);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
     fgets(line, MAXLINE, ficpar);         else
     puts(line);           fprintf(ficgp,"\nset title \"Probability\"\n");
     fputs(line,ficparo);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
   }         i=1;
   ungetc(c,ficpar);         for(k2=1; k2<=nlstate; k2++) {
            k3=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 != k2){
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);               if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);               else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
 /*------------ gnuplot -------------*/               ij=1;
   strcpy(optionfilegnuplot,optionfilefiname);               for(j=3; j <=ncovmodel; j++) {
   strcat(optionfilegnuplot,".gp");                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     printf("Problem with file %s",optionfilegnuplot);                   ij++;
   }                 }
   fclose(ficgp);                 else
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
 /*--------- index.htm --------*/               }
                fprintf(ficgp,")/(1");
   strcpy(optionfilehtm,optionfile);               
   strcat(optionfilehtm,".htm");               for(k1=1; k1 <=nlstate; k1++){   
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
     printf("Problem with %s \n",optionfilehtm), exit(0);                 ij=1;
   }                 for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n                     ij++;
 \n                   }
 Total number of observations=%d <br>\n                   else
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
 <hr  size=\"2\" color=\"#EC5E5E\">                 }
  <ul><li><h4>Parameter files</h4>\n                 fprintf(ficgp,")");
  - 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               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   fclose(fichtm);               i=i+ncovmodel;
              }
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);           } /* end k */
           } /* end k2 */
 /*------------ free_vector  -------------*/       } /* end jk */
  chdir(path);     } /* end ng */
       fflush(ficgp); 
  free_ivector(wav,1,imx);  }  /* end gnuplot */
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    
  free_ivector(num,1,n);  /*************** Moving average **************/
  free_vector(agedc,1,n);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
  /*free_matrix(covar,1,NCOVMAX,1,n);*/  
  fclose(ficparo);    int i, cpt, cptcod;
  fclose(ficres);    int modcovmax =1;
     int mobilavrange, mob;
     double age;
   /*--------------- Prevalence limit --------------*/  
      modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
   strcpy(filerespl,"pl");                             a covariate has 2 modalities */
   strcat(filerespl,fileres);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;      if(mobilav==1) mobilavrange=5; /* default */
   }      else mobilavrange=mobilav;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      for (age=bage; age<=fage; age++)
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);        for (i=1; i<=nlstate;i++)
   fprintf(ficrespl,"#Prevalence limit\n");          for (cptcod=1;cptcod<=modcovmax;cptcod++)
   fprintf(ficrespl,"#Age ");            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      /* We keep the original values on the extreme ages bage, fage and for 
   fprintf(ficrespl,"\n");         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
           we use a 5 terms etc. until the borders are no more concerned. 
   prlim=matrix(1,nlstate,1,nlstate);      */ 
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for (mob=3;mob <=mobilavrange;mob=mob+2){
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for (i=1; i<=nlstate;i++){
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for (cptcod=1;cptcod<=modcovmax;cptcod++){
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   k=0;                for (cpt=1;cpt<=(mob-1)/2;cpt++){
   agebase=ageminpar;                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
   agelim=agemaxpar;                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
   ftolpl=1.e-10;                }
   i1=cptcoveff;              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   if (cptcovn < 1){i1=1;}            }
           }
   for(cptcov=1;cptcov<=i1;cptcov++){        }/* end age */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      }/* end mob */
         k=k+1;    }else return -1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    return 0;
         fprintf(ficrespl,"\n#******");  }/* End movingaverage */
         printf("\n#******");  
         fprintf(ficlog,"\n#******");  
         for(j=1;j<=cptcoveff;j++) {  /************** Forecasting ******************/
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  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){
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* proj1, year, month, day of starting projection 
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       agemin, agemax range of age
         }       dateprev1 dateprev2 range of dates during which prevalence is computed
         fprintf(ficrespl,"******\n");       anproj2 year of en of projection (same day and month as proj1).
         printf("******\n");    */
         fprintf(ficlog,"******\n");    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
            int *popage;
         for (age=agebase; age<=agelim; age++){    double agec; /* generic age */
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
           fprintf(ficrespl,"%.0f",age );    double *popeffectif,*popcount;
           for(i=1; i<=nlstate;i++)    double ***p3mat;
           fprintf(ficrespl," %.5f", prlim[i][i]);    double ***mobaverage;
           fprintf(ficrespl,"\n");    char fileresf[FILENAMELENGTH];
         }  
       }    agelim=AGESUP;
     }    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   fclose(ficrespl);   
     strcpy(fileresf,"f"); 
   /*------------- h Pij x at various ages ------------*/    strcat(fileresf,fileres);
      if((ficresf=fopen(fileresf,"w"))==NULL) {
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      printf("Problem with forecast resultfile: %s\n", fileresf);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    }
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;    printf("Computing forecasting: result on file '%s' \n", fileresf);
   }    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   printf("Computing pij: result on file '%s' \n", filerespij);  
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
    
   stepsize=(int) (stepm+YEARM-1)/YEARM;    if (mobilav!=0) {
   /*if (stepm<=24) stepsize=2;*/      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
   agelim=AGESUP;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   hstepm=stepsize*YEARM; /* Every year of age */        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      }
     }
   /* hstepm=1;   aff par mois*/  
     stepsize=(int) (stepm+YEARM-1)/YEARM;
   k=0;    if (stepm<=12) stepsize=1;
   for(cptcov=1;cptcov<=i1;cptcov++){    if(estepm < stepm){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      printf ("Problem %d lower than %d\n",estepm, stepm);
       k=k+1;    }
         fprintf(ficrespij,"\n#****** ");    else  hstepm=estepm;   
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    hstepm=hstepm/stepm; 
         fprintf(ficrespij,"******\n");    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                         fractional in yp1 */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    anprojmean=yp;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    yp2=modf((yp1*12),&yp);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
           /*      nhstepm=nhstepm*YEARM; aff par mois*/    jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if(mprojmean==0) jprojmean=1;
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      i1=cptcoveff;
           fprintf(ficrespij,"# Age");    if (cptcovn < 1){i1=1;}
           for(i=1; i<=nlstate;i++)    
             for(j=1; j<=nlstate+ndeath;j++)    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
               fprintf(ficrespij," %1d-%1d",i,j);    
           fprintf(ficrespij,"\n");    fprintf(ficresf,"#****** Routine prevforecast **\n");
            for (h=0; h<=nhstepm; h++){  
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  /*            if (h==(int)(YEARM*yearp)){ */
             for(i=1; i<=nlstate;i++)    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
               for(j=1; j<=nlstate+ndeath;j++)      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        k=k+1;
             fprintf(ficrespij,"\n");        fprintf(ficresf,"\n#******");
              }        for(j=1;j<=cptcoveff;j++) {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"\n");        }
         }        fprintf(ficresf,"******\n");
     }        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
   }        for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);            fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
   fclose(ficrespij);        }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
   /*---------- Forecasting ------------------*/          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   if((stepm == 1) && (strcmp(model,".")==0)){  
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);          for (agec=fage; agec>=(ageminpar-1); agec--){ 
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
   }            nhstepm = nhstepm/hstepm; 
   else{            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     erreur=108;            oldm=oldms;savm=savms;
     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);            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
     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);          
   }            for (h=0; h<=nhstepm; h++){
                if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
   /*---------- Health expectancies and variances ------------*/                for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   strcpy(filerest,"t");                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
   strcat(filerest,fileres);              } 
   if((ficrest=fopen(filerest,"w"))==NULL) {              for(j=1; j<=nlstate+ndeath;j++) {
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                ppij=0.;
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;                for(i=1; i<=nlstate;i++) {
   }                  if (mobilav==1) 
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);                  else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
   strcpy(filerese,"e");                  if (h*hstepm/YEARM*stepm== yearp) {
   strcat(filerese,fileres);                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
   if((ficreseij=fopen(filerese,"w"))==NULL) {                  }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                } /* end i */
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                if (h*hstepm/YEARM*stepm==yearp) {
   }                  fprintf(ficresf," %.3f", ppij);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);                }
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);              }/* end j */
             } /* end h */
   strcpy(fileresv,"v");            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcat(fileresv,fileres);          } /* end agec */
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        } /* end yearp */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      } /* end cptcod */
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);    } /* end  cptcov */
   }         
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  
   calagedate=-1;    fclose(ficresf);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  }
   
   k=0;  /************** Forecasting *****not tested NB*************/
   for(cptcov=1;cptcov<=i1;cptcov++){  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){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    
       k=k+1;    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
       fprintf(ficrest,"\n#****** ");    int *popage;
       for(j=1;j<=cptcoveff;j++)    double calagedatem, agelim, kk1, kk2;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double *popeffectif,*popcount;
       fprintf(ficrest,"******\n");    double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
       fprintf(ficreseij,"\n#****** ");    char filerespop[FILENAMELENGTH];
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fprintf(ficreseij,"******\n");    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
       fprintf(ficresvij,"\n#****** ");    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
       for(j=1;j<=cptcoveff;j++)    
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       fprintf(ficresvij,"******\n");    
     
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    strcpy(filerespop,"pop"); 
       oldm=oldms;savm=savms;    strcat(filerespop,fileres);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);      if((ficrespop=fopen(filerespop,"w"))==NULL) {
        printf("Problem with forecast resultfile: %s\n", filerespop);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
       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);    printf("Computing forecasting: result on file '%s' \n", filerespop);
       if(popbased==1){    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);  
        }    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
      if (mobilav!=0) {
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
       fprintf(ficrest,"\n");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       epj=vector(1,nlstate+1);      }
       for(age=bage; age <=fage ;age++){    }
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
         if (popbased==1) {    stepsize=(int) (stepm+YEARM-1)/YEARM;
           for(i=1; i<=nlstate;i++)    if (stepm<=12) stepsize=1;
             prlim[i][i]=probs[(int)age][i][k];    
         }    agelim=AGESUP;
            
         fprintf(ficrest," %4.0f",age);    hstepm=1;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    hstepm=hstepm/stepm; 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    if (popforecast==1) {
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/      if((ficpop=fopen(popfile,"r"))==NULL) {
           }        printf("Problem with population file : %s\n",popfile);exit(0);
           epj[nlstate+1] +=epj[j];        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
         }      } 
       popage=ivector(0,AGESUP);
         for(i=1, vepp=0.;i <=nlstate;i++)      popeffectif=vector(0,AGESUP);
           for(j=1;j <=nlstate;j++)      popcount=vector(0,AGESUP);
             vepp += vareij[i][j][(int)age];      
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));      i=1;   
         for(j=1;j <=nlstate;j++){      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));     
         }      imx=i;
         fprintf(ficrest,"\n");      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
       }    }
     }  
   }    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
 free_matrix(mint,1,maxwav,1,n);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);        k=k+1;
     free_vector(weight,1,n);        fprintf(ficrespop,"\n#******");
   fclose(ficreseij);        for(j=1;j<=cptcoveff;j++) {
   fclose(ficresvij);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   fclose(ficrest);        }
   fclose(ficpar);        fprintf(ficrespop,"******\n");
   free_vector(epj,1,nlstate+1);        fprintf(ficrespop,"# Age");
          for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
   /*------- Variance limit prevalence------*/          if (popforecast==1)  fprintf(ficrespop," [Population]");
         
   strcpy(fileresvpl,"vpl");        for (cpt=0; cpt<=0;cpt++) { 
   strcat(fileresvpl,fileres);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
     exit(0);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   }            nhstepm = nhstepm/hstepm; 
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);            
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   k=0;            oldm=oldms;savm=savms;
   for(cptcov=1;cptcov<=i1;cptcov++){            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          
       k=k+1;            for (h=0; h<=nhstepm; h++){
       fprintf(ficresvpl,"\n#****** ");              if (h==(int) (calagedatem+YEARM*cpt)) {
       for(j=1;j<=cptcoveff;j++)                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              } 
       fprintf(ficresvpl,"******\n");              for(j=1; j<=nlstate+ndeath;j++) {
                      kk1=0.;kk2=0;
       varpl=matrix(1,nlstate,(int) bage, (int) fage);                for(i=1; i<=nlstate;i++) {              
       oldm=oldms;savm=savms;                  if (mobilav==1) 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
     }                  else {
  }                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
   fclose(ficresvpl);                }
                 if (h==(int)(calagedatem+12*cpt)){
   /*---------- End : free ----------------*/                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);                    /*fprintf(ficrespop," %.3f", kk1);
                        if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);                }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);              }
                for(i=1; i<=nlstate;i++){
                  kk1=0.;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);                  for(j=1; j<=nlstate;j++){
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);                  }
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
                }
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
   free_matrix(agev,1,maxwav,1,imx);                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);            }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fprintf(fichtm,"\n</body>");          }
   fclose(fichtm);        }
   fclose(ficgp);   
      /******/
   
   if(erreur >0){        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
     printf("End of Imach with error or warning %d\n",erreur);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   }else{            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
    printf("End of Imach\n");            nhstepm = nhstepm/hstepm; 
    fprintf(ficlog,"End of Imach\n");            
   }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("See log file on %s\n",filelog);            oldm=oldms;savm=savms;
   fclose(ficlog);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */            for (h=0; h<=nhstepm; h++){
                if (h==(int) (calagedatem+YEARM*cpt)) {
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   /*printf("Total time was %d uSec.\n", total_usecs);*/              } 
   /*------ End -----------*/              for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
  end:                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
 #ifdef windows                }
   /* chdir(pathcd);*/                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
 #endif              }
  /*system("wgnuplot graph.plt");*/            }
  /*system("../gp37mgw/wgnuplot graph.plt");*/            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  /*system("cd ../gp37mgw");*/          }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        }
  strcpy(plotcmd,GNUPLOTPROGRAM);     } 
  strcat(plotcmd," ");    }
  strcat(plotcmd,optionfilegnuplot);   
  system(plotcmd);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
 #ifdef windows    if (popforecast==1) {
   while (z[0] != 'q') {      free_ivector(popage,0,AGESUP);
     /* chdir(path); */      free_vector(popeffectif,0,AGESUP);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");      free_vector(popcount,0,AGESUP);
     scanf("%s",z);    }
     if (z[0] == 'c') system("./imach");    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     else if (z[0] == 'e') system(optionfilehtm);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     else if (z[0] == 'g') system(plotcmd);    fclose(ficrespop);
     else if (z[0] == 'q') exit(0);  } /* End of popforecast */
   }  
 #endif  int fileappend(FILE *fichier, char *optionfich)
 }  {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           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,double agemortsup){
     int i,k;
   
     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>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     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 linei, month, year,iout;
     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];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     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]; 
     char **bp, *tok, *val; /* pathtot */
     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;
     int agemortsup;
     float  sumlpop=0.;
     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  *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: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     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], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     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 while opening datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem while opening 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;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
           exit(1);
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           exit(1);
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(1);
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(1);
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         exit(1);
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           exit(1);
         }
         covar[j][i]=(double)(lval);
         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;
     } /* End loop reading  data */
     fclose(fic);
     /* 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 parameters 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);*/
   
       /*  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 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           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\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\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,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             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,strstart);
   
     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 (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    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;
           }else 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]=0.0268; p[NDIM]=0.083;
       /*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]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* 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,pathcd); /* 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  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (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*/
       pstamp(ficrespij);
       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,strstart);
   
       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 Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: 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(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       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#****** ");
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\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, strstart);  
           cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           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, strstart);
           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, strstart);
           }
   
           pstamp(ficrest);
           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( 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(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (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,strstart);
           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(prlim,1,nlstate,1,nlstate);
       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);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     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\nLocal time 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 -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n 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.1.50  
changed lines
  Added in v.1.122


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