Diff for /imach/src/imach.c between versions 1.46 and 1.122

version 1.46, 2002/05/30 17:44:35 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
   
     Revision 1.106  2006/01/19 13:24:36  brouard
 int erreur; /* Error number */    Some cleaning and links added in html output
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.105  2006/01/05 20:23:19  lievre
 int npar=NPARMAX;    *** empty log message ***
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.104  2005/09/30 16:11:43  lievre
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    (Module): sump fixed, loop imx fixed, and simplifications.
 int popbased=0;    (Module): If the status is missing at the last wave but we know
     that the person is alive, then we can code his/her status as -2
 int *wav; /* Number of waves for this individuual 0 is possible */    (instead of missing=-1 in earlier versions) and his/her
 int maxwav; /* Maxim number of waves */    contributions to the likelihood is 1 - Prob of dying from last
 int jmin, jmax; /* min, max spacing between 2 waves */    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 int mle, weightopt;    the healthy state at last known wave). Version is 0.98
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.103  2005/09/30 15:54:49  lievre
 double jmean; /* Mean space between 2 waves */    (Module): sump fixed, loop imx fixed, and simplifications.
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.102  2004/09/15 17:31:30  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Add the possibility to read data file including tab characters.
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  
 FILE *ficreseij;    Revision 1.101  2004/09/15 10:38:38  brouard
   char filerese[FILENAMELENGTH];    Fix on curr_time
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Revision 1.100  2004/07/12 18:29:06  brouard
  FILE  *ficresvpl;    Add version for Mac OS X. Just define UNIX in Makefile
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.99  2004/06/05 08:57:40  brouard
 #define NR_END 1    *** empty log message ***
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.98  2004/05/16 15:05:56  brouard
     New version 0.97 . First attempt to estimate force of mortality
 #define NRANSI    directly from the data i.e. without the need of knowing the health
 #define ITMAX 200    state at each age, but using a Gompertz model: log u =a + b*age .
     This is the basic analysis of mortality and should be done before any
 #define TOL 2.0e-4    other analysis, in order to test if the mortality estimated from the
     cross-longitudinal survey is different from the mortality estimated
 #define CGOLD 0.3819660    from other sources like vital statistic data.
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    The same imach parameter file can be used but the option for mle should be -3.
   
 #define GOLD 1.618034    Agnès, who wrote this part of the code, tried to keep most of the
 #define GLIMIT 100.0    former routines in order to include the new code within the former code.
 #define TINY 1.0e-20  
     The output is very simple: only an estimate of the intercept and of
 static double maxarg1,maxarg2;    the slope with 95% confident intervals.
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Current limitations:
      A) Even if you enter covariates, i.e. with the
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define rint(a) floor(a+0.5)    B) There is no computation of Life Expectancy nor Life Table.
   
 static double sqrarg;    Revision 1.97  2004/02/20 13:25:42  lievre
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Version 0.96d. Population forecasting command line is (temporarily)
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    suppressed.
   
 int imx;    Revision 1.96  2003/07/15 15:38:55  brouard
 int stepm;    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 /* Stepm, step in month: minimum step interpolation*/    rewritten within the same printf. Workaround: many printfs.
   
 int estepm;    Revision 1.95  2003/07/08 07:54:34  brouard
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    * imach.c (Repository):
     (Repository): Using imachwizard code to output a more meaningful covariance
 int m,nb;    matrix (cov(a12,c31) instead of numbers.
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.94  2003/06/27 13:00:02  brouard
 double **pmmij, ***probs, ***mobaverage;    Just cleaning
 double dateintmean=0;  
     Revision 1.93  2003/06/25 16:33:55  brouard
 double *weight;    (Module): On windows (cygwin) function asctime_r doesn't
 int **s; /* Status */    exist so I changed back to asctime which exists.
 double *agedc, **covar, idx;    (Module): Version 0.96b
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.92  2003/06/25 16:30:45  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    (Module): On windows (cygwin) function asctime_r doesn't
 double ftolhess; /* Tolerance for computing hessian */    exist so I changed back to asctime which exists.
   
 /**************** split *************************/    Revision 1.91  2003/06/25 15:30:29  brouard
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    * imach.c (Repository): Duplicated warning errors corrected.
 {    (Repository): Elapsed time after each iteration is now output. It
    char *s;                             /* pointer */    helps to forecast when convergence will be reached. Elapsed time
    int  l1, l2;                         /* length counters */    is stamped in powell.  We created a new html file for the graphs
     concerning matrix of covariance. It has extension -cov.htm.
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.90  2003/06/24 12:34:15  brouard
 #ifdef windows    (Module): Some bugs corrected for windows. Also, when
    s = strrchr( path, '\\' );           /* find last / */    mle=-1 a template is output in file "or"mypar.txt with the design
 #else    of the covariance matrix to be input.
    s = strrchr( path, '/' );            /* find last / */  
 #endif    Revision 1.89  2003/06/24 12:30:52  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    (Module): Some bugs corrected for windows. Also, when
 #if     defined(__bsd__)                /* get current working directory */    mle=-1 a template is output in file "or"mypar.txt with the design
       extern char       *getwd( );    of the covariance matrix to be input.
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.88  2003/06/23 17:54:56  brouard
 #else    * 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.
       extern char       *getcwd( );  
     Revision 1.87  2003/06/18 12:26:01  brouard
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Version 0.96
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.86  2003/06/17 20:04:08  brouard
       }    (Module): Change position of html and gnuplot routines and added
       strcpy( name, path );             /* we've got it */    routine fileappend.
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Revision 1.85  2003/06/17 13:12:43  brouard
       l2 = strlen( s );                 /* length of filename */    * imach.c (Repository): Check when date of death was earlier that
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    current date of interview. It may happen when the death was just
       strcpy( name, s );                /* save file name */    prior to the death. In this case, dh was negative and likelihood
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    was wrong (infinity). We still send an "Error" but patch by
       dirc[l1-l2] = 0;                  /* add zero */    assuming that the date of death was just one stepm after the
    }    interview.
    l1 = strlen( dirc );                 /* length of directory */    (Repository): Because some people have very long ID (first column)
 #ifdef windows    we changed int to long in num[] and we added a new lvector for
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    memory allocation. But we also truncated to 8 characters (left
 #else    truncation)
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    (Repository): No more line truncation errors.
 #endif  
    s = strrchr( name, '.' );            /* find last / */    Revision 1.84  2003/06/13 21:44:43  brouard
    s++;    * imach.c (Repository): Replace "freqsummary" at a correct
    strcpy(ext,s);                       /* save extension */    place. It differs from routine "prevalence" which may be called
    l1= strlen( name);    many times. Probs is memory consuming and must be used with
    l2= strlen( s)+1;    parcimony.
    strncpy( finame, name, l1-l2);    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */    Revision 1.83  2003/06/10 13:39:11  lievre
 }    *** empty log message ***
   
     Revision 1.82  2003/06/05 15:57:20  brouard
 /******************************************/    Add log in  imach.c and  fullversion number is now printed.
   
 void replace(char *s, char*t)  */
 {  /*
   int i;     Interpolated Markov Chain
   int lg=20;  
   i=0;    Short summary of the programme:
   lg=strlen(t);    
   for(i=0; i<= lg; i++) {    This program computes Healthy Life Expectancies from
     (s[i] = t[i]);    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     if (t[i]== '\\') s[i]='/';    first survey ("cross") where individuals from different ages are
   }    interviewed on their health status or degree of disability (in the
 }    case of a health survey which is our main interest) -2- at least a
     second wave of interviews ("longitudinal") which measure each change
 int nbocc(char *s, char occ)    (if any) in individual health status.  Health expectancies are
 {    computed from the time spent in each health state according to a
   int i,j=0;    model. More health states you consider, more time is necessary to reach the
   int lg=20;    Maximum Likelihood of the parameters involved in the model.  The
   i=0;    simplest model is the multinomial logistic model where pij is the
   lg=strlen(s);    probability to be observed in state j at the second wave
   for(i=0; i<= lg; i++) {    conditional to be observed in state i at the first wave. Therefore
   if  (s[i] == occ ) j++;    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
   return j;    complex model than "constant and age", you should modify the program
 }    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
 void cutv(char *u,char *v, char*t, char occ)    convergence.
 {  
   int i,lg,j,p=0;    The advantage of this computer programme, compared to a simple
   i=0;    multinomial logistic model, is clear when the delay between waves is not
   for(j=0; j<=strlen(t)-1; j++) {    identical for each individual. Also, if a individual missed an
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    intermediate interview, the information is lost, but taken into
   }    account using an interpolation or extrapolation.  
   
   lg=strlen(t);    hPijx is the probability to be observed in state i at age x+h
   for(j=0; j<p; j++) {    conditional to the observed state i at age x. The delay 'h' can be
     (u[j] = t[j]);    split into an exact number (nh*stepm) of unobserved intermediate
   }    states. This elementary transition (by month, quarter,
      u[p]='\0';    semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
    for(j=0; j<= lg; j++) {    and the contribution of each individual to the likelihood is simply
     if (j>=(p+1))(v[j-p-1] = t[j]);    hPijx.
   }  
 }    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the period (stable) prevalence. 
 /********************** nrerror ********************/    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 void nrerror(char error_text[])             Institut national d'études démographiques, Paris.
 {    This software have been partly granted by Euro-REVES, a concerted action
   fprintf(stderr,"ERREUR ...\n");    from the European Union.
   fprintf(stderr,"%s\n",error_text);    It is copyrighted identically to a GNU software product, ie programme and
   exit(1);    software can be distributed freely for non commercial use. Latest version
 }    can be accessed at http://euroreves.ined.fr/imach .
 /*********************** vector *******************/  
 double *vector(int nl, int nh)    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
   double *v;    
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    **********************************************************************/
   if (!v) nrerror("allocation failure in vector");  /*
   return v-nl+NR_END;    main
 }    read parameterfile
     read datafile
 /************************ free vector ******************/    concatwav
 void free_vector(double*v, int nl, int nh)    freqsummary
 {    if (mle >= 1)
   free((FREE_ARG)(v+nl-NR_END));      mlikeli
 }    print results files
     if mle==1 
 /************************ivector *******************************/       computes hessian
 int *ivector(long nl,long nh)    read end of parameter file: agemin, agemax, bage, fage, estepm
 {        begin-prev-date,...
   int *v;    open gnuplot file
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    open html file
   if (!v) nrerror("allocation failure in ivector");    period (stable) prevalence
   return v-nl+NR_END;     for age prevalim()
 }    h Pij x
     variance of p varprob
 /******************free ivector **************************/    forecasting if prevfcast==1 prevforecast call prevalence()
 void free_ivector(int *v, long nl, long nh)    health expectancies
 {    Variance-covariance of DFLE
   free((FREE_ARG)(v+nl-NR_END));    prevalence()
 }     movingaverage()
     varevsij() 
 /******************* imatrix *******************************/    if popbased==1 varevsij(,popbased)
 int **imatrix(long nrl, long nrh, long ncl, long nch)    total life expectancies
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Variance of period (stable) prevalence
 {   end
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  */
   int **m;  
    
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));   
   if (!m) nrerror("allocation failure 1 in matrix()");  #include <math.h>
   m += NR_END;  #include <stdio.h>
   m -= nrl;  #include <stdlib.h>
    #include <string.h>
    #include <unistd.h>
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #include <limits.h>
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #include <sys/types.h>
   m[nrl] += NR_END;  #include <sys/stat.h>
   m[nrl] -= ncl;  #include <errno.h>
    extern int errno;
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    /* #include <sys/time.h> */
   /* return pointer to array of pointers to rows */  #include <time.h>
   return m;  #include "timeval.h"
 }  
   /* #include <libintl.h> */
 /****************** free_imatrix *************************/  /* #define _(String) gettext (String) */
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  #define MAXLINE 256
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */  #define GNUPLOTPROGRAM "gnuplot"
 {  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #define FILENAMELENGTH 132
   free((FREE_ARG) (m+nrl-NR_END));  
 }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 {  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;  #define NINTERVMAX 8
   #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   if (!m) nrerror("allocation failure 1 in matrix()");  #define NCOVMAX 8 /* Maximum number of covariates */
   m += NR_END;  #define MAXN 20000
   m -= nrl;  #define YEARM 12. /* Number of months per year */
   #define AGESUP 130
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define AGEBASE 40
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   m[nrl] += NR_END;  #ifdef UNIX
   m[nrl] -= ncl;  #define DIRSEPARATOR '/'
   #define CHARSEPARATOR "/"
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define ODIRSEPARATOR '\\'
   return m;  #else
 }  #define DIRSEPARATOR '\\'
   #define CHARSEPARATOR "\\"
 /*************************free matrix ************************/  #define ODIRSEPARATOR '/'
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  #endif
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  /* $Id$ */
   free((FREE_ARG)(m+nrl-NR_END));  /* $State$ */
 }  
   char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
 /******************* ma3x *******************************/  char fullversion[]="$Revision$ $Date$"; 
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  char strstart[80];
 {  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   double ***m;  int nvar;
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int npar=NPARMAX;
   if (!m) nrerror("allocation failure 1 in matrix()");  int nlstate=2; /* Number of live states */
   m += NR_END;  int ndeath=1; /* Number of dead states */
   m -= nrl;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int *wav; /* Number of waves for this individuual 0 is possible */
   m[nrl] += NR_END;  int maxwav; /* Maxim number of waves */
   m[nrl] -= ncl;  int jmin, jmax; /* min, max spacing between 2 waves */
   int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int gipmx, gsw; /* Global variables on the number of contributions 
                      to the likelihood and the sum of weights (done by funcone)*/
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  int mle, weightopt;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   m[nrl][ncl] += NR_END;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   m[nrl][ncl] -= nll;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   for (j=ncl+1; j<=nch; j++)             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     m[nrl][j]=m[nrl][j-1]+nlay;  double jmean; /* Mean space between 2 waves */
    double **oldm, **newm, **savm; /* Working pointers to matrices */
   for (i=nrl+1; i<=nrh; i++) {  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
     for (j=ncl+1; j<=nch; j++)  FILE *ficlog, *ficrespow;
       m[i][j]=m[i][j-1]+nlay;  int globpr; /* Global variable for printing or not */
   }  double fretone; /* Only one call to likelihood */
   return m;  long ipmx; /* Number of contributions */
 }  double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
 /*************************free ma3x ************************/  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  FILE *ficresilk;
 {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  FILE *ficresprobmorprev;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  FILE *fichtm, *fichtmcov; /* Html File */
   free((FREE_ARG)(m+nrl-NR_END));  FILE *ficreseij;
 }  char filerese[FILENAMELENGTH];
   FILE *ficresstdeij;
 /***************** f1dim *************************/  char fileresstde[FILENAMELENGTH];
 extern int ncom;  FILE *ficrescveij;
 extern double *pcom,*xicom;  char filerescve[FILENAMELENGTH];
 extern double (*nrfunc)(double []);  FILE  *ficresvij;
    char fileresv[FILENAMELENGTH];
 double f1dim(double x)  FILE  *ficresvpl;
 {  char fileresvpl[FILENAMELENGTH];
   int j;  char title[MAXLINE];
   double f;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   double *xt;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
    char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   xt=vector(1,ncom);  char command[FILENAMELENGTH];
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  int  outcmd=0;
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   return f;  
 }  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
 /*****************brent *************************/  char fileregp[FILENAMELENGTH];
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  char popfile[FILENAMELENGTH];
 {  
   int iter;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   double a,b,d,etemp;  
   double fu,fv,fw,fx;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   double ftemp;  struct timezone tzp;
   double p,q,r,tol1,tol2,u,v,w,x,xm;  extern int gettimeofday();
   double e=0.0;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
    long time_value;
   a=(ax < cx ? ax : cx);  extern long time();
   b=(ax > cx ? ax : cx);  char strcurr[80], strfor[80];
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);  char *endptr;
   for (iter=1;iter<=ITMAX;iter++) {  long lval;
     xm=0.5*(a+b);  double dval;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  #define NR_END 1
     printf(".");fflush(stdout);  #define FREE_ARG char*
 #ifdef DEBUG  #define FTOL 1.0e-10
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  #define NRANSI 
 #endif  #define ITMAX 200 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  #define TOL 2.0e-4 
       return fx;  
     }  #define CGOLD 0.3819660 
     ftemp=fu;  #define ZEPS 1.0e-10 
     if (fabs(e) > tol1) {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);  #define GOLD 1.618034 
       p=(x-v)*q-(x-w)*r;  #define GLIMIT 100.0 
       q=2.0*(q-r);  #define TINY 1.0e-20 
       if (q > 0.0) p = -p;  
       q=fabs(q);  static double maxarg1,maxarg2;
       etemp=e;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       e=d;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       else {  #define rint(a) floor(a+0.5)
         d=p/q;  
         u=x+d;  static double sqrarg;
         if (u-a < tol2 || b-u < tol2)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
           d=SIGN(tol1,xm-x);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       }  int agegomp= AGEGOMP;
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  int imx; 
     }  int stepm=1;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  /* Stepm, step in month: minimum step interpolation*/
     fu=(*f)(u);  
     if (fu <= fx) {  int estepm;
       if (u >= x) a=x; else b=x;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  int m,nb;
         } else {  long *num;
           if (u < x) a=u; else b=u;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
           if (fu <= fw || w == x) {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
             v=w;  double **pmmij, ***probs;
             w=u;  double *ageexmed,*agecens;
             fv=fw;  double dateintmean=0;
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {  double *weight;
             v=u;  int **s; /* Status */
             fv=fu;  double *agedc, **covar, idx;
           }  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
         }  double *lsurv, *lpop, *tpop;
   }  
   nrerror("Too many iterations in brent");  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   *xmin=x;  double ftolhess; /* Tolerance for computing hessian */
   return fx;  
 }  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 /****************** mnbrak ***********************/  {
     /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,       the name of the file (name), its extension only (ext) and its first part of the name (finame)
             double (*func)(double))    */ 
 {    char  *ss;                            /* pointer */
   double ulim,u,r,q, dum;    int   l1, l2;                         /* length counters */
   double fu;  
      l1 = strlen(path );                   /* length of path */
   *fa=(*func)(*ax);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   *fb=(*func)(*bx);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   if (*fb > *fa) {    if ( ss == NULL ) {                   /* no directory, so determine current directory */
     SHFT(dum,*ax,*bx,dum)      strcpy( name, path );               /* we got the fullname name because no directory */
       SHFT(dum,*fb,*fa,dum)      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       }        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   *cx=(*bx)+GOLD*(*bx-*ax);      /* get current working directory */
   *fc=(*func)(*cx);      /*    extern  char* getcwd ( char *buf , int len);*/
   while (*fb > *fc) {      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     r=(*bx-*ax)*(*fb-*fc);        return( GLOCK_ERROR_GETCWD );
     q=(*bx-*cx)*(*fb-*fa);      }
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      /* got dirc from getcwd*/
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));      printf(" DIRC = %s \n",dirc);
     ulim=(*bx)+GLIMIT*(*cx-*bx);    } else {                              /* strip direcotry from path */
     if ((*bx-u)*(u-*cx) > 0.0) {      ss++;                               /* after this, the filename */
       fu=(*func)(u);      l2 = strlen( ss );                  /* length of filename */
     } else if ((*cx-u)*(u-ulim) > 0.0) {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       fu=(*func)(u);      strcpy( name, ss );         /* save file name */
       if (fu < *fc) {      strncpy( dirc, path, l1 - l2 );     /* now the directory */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      dirc[l1-l2] = 0;                    /* add zero */
           SHFT(*fb,*fc,fu,(*func)(u))      printf(" DIRC2 = %s \n",dirc);
           }    }
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    /* We add a separator at the end of dirc if not exists */
       u=ulim;    l1 = strlen( dirc );                  /* length of directory */
       fu=(*func)(u);    if( dirc[l1-1] != DIRSEPARATOR ){
     } else {      dirc[l1] =  DIRSEPARATOR;
       u=(*cx)+GOLD*(*cx-*bx);      dirc[l1+1] = 0; 
       fu=(*func)(u);      printf(" DIRC3 = %s \n",dirc);
     }    }
     SHFT(*ax,*bx,*cx,u)    ss = strrchr( name, '.' );            /* find last / */
       SHFT(*fa,*fb,*fc,fu)    if (ss >0){
       }      ss++;
 }      strcpy(ext,ss);                     /* save extension */
       l1= strlen( name);
 /*************** linmin ************************/      l2= strlen(ss)+1;
       strncpy( finame, name, l1-l2);
 int ncom;      finame[l1-l2]= 0;
 double *pcom,*xicom;    }
 double (*nrfunc)(double []);  
      return( 0 );                          /* we're done */
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  }
 {  
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);  /******************************************/
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  void replace_back_to_slash(char *s, char*t)
               double *fc, double (*func)(double));  {
   int j;    int i;
   double xx,xmin,bx,ax;    int lg=0;
   double fx,fb,fa;    i=0;
      lg=strlen(t);
   ncom=n;    for(i=0; i<= lg; i++) {
   pcom=vector(1,n);      (s[i] = t[i]);
   xicom=vector(1,n);      if (t[i]== '\\') s[i]='/';
   nrfunc=func;    }
   for (j=1;j<=n;j++) {  }
     pcom[j]=p[j];  
     xicom[j]=xi[j];  int nbocc(char *s, char occ)
   }  {
   ax=0.0;    int i,j=0;
   xx=1.0;    int lg=20;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    i=0;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    lg=strlen(s);
 #ifdef DEBUG    for(i=0; i<= lg; i++) {
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    if  (s[i] == occ ) j++;
 #endif    }
   for (j=1;j<=n;j++) {    return j;
     xi[j] *= xmin;  }
     p[j] += xi[j];  
   }  void cutv(char *u,char *v, char*t, char occ)
   free_vector(xicom,1,n);  {
   free_vector(pcom,1,n);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
 }       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
        gives u="abcedf" and v="ghi2j" */
 /*************** powell ************************/    int i,lg,j,p=0;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    i=0;
             double (*func)(double []))    for(j=0; j<=strlen(t)-1; j++) {
 {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   void linmin(double p[], double xi[], int n, double *fret,    }
               double (*func)(double []));  
   int i,ibig,j;    lg=strlen(t);
   double del,t,*pt,*ptt,*xit;    for(j=0; j<p; j++) {
   double fp,fptt;      (u[j] = t[j]);
   double *xits;    }
   pt=vector(1,n);       u[p]='\0';
   ptt=vector(1,n);  
   xit=vector(1,n);     for(j=0; j<= lg; j++) {
   xits=vector(1,n);      if (j>=(p+1))(v[j-p-1] = t[j]);
   *fret=(*func)(p);    }
   for (j=1;j<=n;j++) pt[j]=p[j];  }
   for (*iter=1;;++(*iter)) {  
     fp=(*fret);  /********************** nrerror ********************/
     ibig=0;  
     del=0.0;  void nrerror(char error_text[])
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  {
     for (i=1;i<=n;i++)    fprintf(stderr,"ERREUR ...\n");
       printf(" %d %.12f",i, p[i]);    fprintf(stderr,"%s\n",error_text);
     printf("\n");    exit(EXIT_FAILURE);
     for (i=1;i<=n;i++) {  }
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  /*********************** vector *******************/
       fptt=(*fret);  double *vector(int nl, int nh)
 #ifdef DEBUG  {
       printf("fret=%lf \n",*fret);    double *v;
 #endif    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       printf("%d",i);fflush(stdout);    if (!v) nrerror("allocation failure in vector");
       linmin(p,xit,n,fret,func);    return v-nl+NR_END;
       if (fabs(fptt-(*fret)) > del) {  }
         del=fabs(fptt-(*fret));  
         ibig=i;  /************************ free vector ******************/
       }  void free_vector(double*v, int nl, int nh)
 #ifdef DEBUG  {
       printf("%d %.12e",i,(*fret));    free((FREE_ARG)(v+nl-NR_END));
       for (j=1;j<=n;j++) {  }
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);  /************************ivector *******************************/
       }  int *ivector(long nl,long nh)
       for(j=1;j<=n;j++)  {
         printf(" p=%.12e",p[j]);    int *v;
       printf("\n");    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 #endif    if (!v) nrerror("allocation failure in ivector");
     }    return v-nl+NR_END;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  }
 #ifdef DEBUG  
       int k[2],l;  /******************free ivector **************************/
       k[0]=1;  void free_ivector(int *v, long nl, long nh)
       k[1]=-1;  {
       printf("Max: %.12e",(*func)(p));    free((FREE_ARG)(v+nl-NR_END));
       for (j=1;j<=n;j++)  }
         printf(" %.12e",p[j]);  
       printf("\n");  /************************lvector *******************************/
       for(l=0;l<=1;l++) {  long *lvector(long nl,long nh)
         for (j=1;j<=n;j++) {  {
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    long *v;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
         }    if (!v) nrerror("allocation failure in ivector");
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    return v-nl+NR_END;
       }  }
 #endif  
   /******************free lvector **************************/
   void free_lvector(long *v, long nl, long nh)
       free_vector(xit,1,n);  {
       free_vector(xits,1,n);    free((FREE_ARG)(v+nl-NR_END));
       free_vector(ptt,1,n);  }
       free_vector(pt,1,n);  
       return;  /******************* imatrix *******************************/
     }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     for (j=1;j<=n;j++) {  { 
       ptt[j]=2.0*p[j]-pt[j];    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       xit[j]=p[j]-pt[j];    int **m; 
       pt[j]=p[j];    
     }    /* allocate pointers to rows */ 
     fptt=(*func)(ptt);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (fptt < fp) {    if (!m) nrerror("allocation failure 1 in matrix()"); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    m += NR_END; 
       if (t < 0.0) {    m -= nrl; 
         linmin(p,xit,n,fret,func);    
         for (j=1;j<=n;j++) {    
           xi[j][ibig]=xi[j][n];    /* allocate rows and set pointers to them */ 
           xi[j][n]=xit[j];    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
         }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 #ifdef DEBUG    m[nrl] += NR_END; 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    m[nrl] -= ncl; 
         for(j=1;j<=n;j++)    
           printf(" %.12e",xit[j]);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
         printf("\n");    
 #endif    /* return pointer to array of pointers to rows */ 
       }    return m; 
     }  } 
   }  
 }  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
 /**** Prevalence limit ****************/        int **m;
         long nch,ncl,nrh,nrl; 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)       /* free an int matrix allocated by imatrix() */ 
 {  { 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
      matrix by transitions matrix until convergence is reached */    free((FREE_ARG) (m+nrl-NR_END)); 
   } 
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;  /******************* matrix *******************************/
   double **matprod2();  double **matrix(long nrl, long nrh, long ncl, long nch)
   double **out, cov[NCOVMAX], **pmij();  {
   double **newm;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   double agefin, delaymax=50 ; /* Max number of years to converge */    double **m;
   
   for (ii=1;ii<=nlstate+ndeath;ii++)    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     for (j=1;j<=nlstate+ndeath;j++){    if (!m) nrerror("allocation failure 1 in matrix()");
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    m += NR_END;
     }    m -= nrl;
   
    cov[1]=1.;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
      if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    m[nrl] += NR_END;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    m[nrl] -= ncl;
     newm=savm;  
     /* Covariates have to be included here again */    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
      cov[2]=agefin;    return m;
      /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       for (k=1; k<=cptcovn;k++) {     */
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  }
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  
       }  /*************************free matrix ************************/
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       for (k=1; k<=cptcovprod;k++)  {
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     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]);*/  
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  /******************* ma3x *******************************/
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   {
     savm=oldm;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     oldm=newm;    double ***m;
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       min=1.;    if (!m) nrerror("allocation failure 1 in matrix()");
       max=0.;    m += NR_END;
       for(i=1; i<=nlstate; i++) {    m -= nrl;
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         prlim[i][j]= newm[i][j]/(1-sumnew);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         max=FMAX(max,prlim[i][j]);    m[nrl] += NR_END;
         min=FMIN(min,prlim[i][j]);    m[nrl] -= ncl;
       }  
       maxmin=max-min;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       maxmax=FMAX(maxmax,maxmin);  
     }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     if(maxmax < ftolpl){    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       return prlim;    m[nrl][ncl] += NR_END;
     }    m[nrl][ncl] -= nll;
   }    for (j=ncl+1; j<=nch; j++) 
 }      m[nrl][j]=m[nrl][j-1]+nlay;
     
 /*************** transition probabilities ***************/    for (i=nrl+1; i<=nrh; i++) {
       m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      for (j=ncl+1; j<=nch; j++) 
 {        m[i][j]=m[i][j-1]+nlay;
   double s1, s2;    }
   /*double t34;*/    return m; 
   int i,j,j1, nc, ii, jj;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
              &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     for(i=1; i<= nlstate; i++){    */
     for(j=1; j<i;j++){  }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         /*s2 += param[i][j][nc]*cov[nc];*/  /*************************free ma3x ************************/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  {
       }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       ps[i][j]=s2;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    free((FREE_ARG)(m+nrl-NR_END));
     }  }
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /*************** function subdirf ***********/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  char *subdirf(char fileres[])
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  {
       }    /* Caution optionfilefiname is hidden */
       ps[i][j]=s2;    strcpy(tmpout,optionfilefiname);
     }    strcat(tmpout,"/"); /* Add to the right */
   }    strcat(tmpout,fileres);
     /*ps[3][2]=1;*/    return tmpout;
   }
   for(i=1; i<= nlstate; i++){  
      s1=0;  /*************** function subdirf2 ***********/
     for(j=1; j<i; j++)  char *subdirf2(char fileres[], char *preop)
       s1+=exp(ps[i][j]);  {
     for(j=i+1; j<=nlstate+ndeath; j++)    
       s1+=exp(ps[i][j]);    /* Caution optionfilefiname is hidden */
     ps[i][i]=1./(s1+1.);    strcpy(tmpout,optionfilefiname);
     for(j=1; j<i; j++)    strcat(tmpout,"/");
       ps[i][j]= exp(ps[i][j])*ps[i][i];    strcat(tmpout,preop);
     for(j=i+1; j<=nlstate+ndeath; j++)    strcat(tmpout,fileres);
       ps[i][j]= exp(ps[i][j])*ps[i][i];    return tmpout;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  }
   } /* end i */  
   /*************** function subdirf3 ***********/
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  char *subdirf3(char fileres[], char *preop, char *preop2)
     for(jj=1; jj<= nlstate+ndeath; jj++){  {
       ps[ii][jj]=0;    
       ps[ii][ii]=1;    /* Caution optionfilefiname is hidden */
     }    strcpy(tmpout,optionfilefiname);
   }    strcat(tmpout,"/");
     strcat(tmpout,preop);
     strcat(tmpout,preop2);
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    strcat(tmpout,fileres);
     for(jj=1; jj<= nlstate+ndeath; jj++){    return tmpout;
      printf("%lf ",ps[ii][jj]);  }
    }  
     printf("\n ");  /***************** f1dim *************************/
     }  extern int ncom; 
     printf("\n ");printf("%lf ",cov[2]);*/  extern double *pcom,*xicom;
 /*  extern double (*nrfunc)(double []); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);   
   goto end;*/  double f1dim(double x) 
     return ps;  { 
 }    int j; 
     double f;
 /**************** Product of 2 matrices ******************/    double *xt; 
    
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    xt=vector(1,ncom); 
 {    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    f=(*nrfunc)(xt); 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    free_vector(xt,1,ncom); 
   /* in, b, out are matrice of pointers which should have been initialized    return f; 
      before: only the contents of out is modified. The function returns  } 
      a pointer to pointers identical to out */  
   long i, j, k;  /*****************brent *************************/
   for(i=nrl; i<= nrh; i++)  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     for(k=ncolol; k<=ncoloh; k++)  { 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    int iter; 
         out[i][k] +=in[i][j]*b[j][k];    double a,b,d,etemp;
     double fu,fv,fw,fx;
   return out;    double ftemp;
 }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     double e=0.0; 
    
 /************* Higher Matrix Product ***************/    a=(ax < cx ? ax : cx); 
     b=(ax > cx ? ax : cx); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    x=w=v=bx; 
 {    fw=fv=fx=(*f)(x); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    for (iter=1;iter<=ITMAX;iter++) { 
      duration (i.e. until      xm=0.5*(a+b); 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
      (typically every 2 years instead of every month which is too big).      printf(".");fflush(stdout);
      Model is determined by parameters x and covariates have to be      fprintf(ficlog,".");fflush(ficlog);
      included manually here.  #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);
       /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   int i, j, d, h, k;  #endif
   double **out, cov[NCOVMAX];      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   double **newm;        *xmin=x; 
         return fx; 
   /* Hstepm could be zero and should return the unit matrix */      } 
   for (i=1;i<=nlstate+ndeath;i++)      ftemp=fu;
     for (j=1;j<=nlstate+ndeath;j++){      if (fabs(e) > tol1) { 
       oldm[i][j]=(i==j ? 1.0 : 0.0);        r=(x-w)*(fx-fv); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);        q=(x-v)*(fx-fw); 
     }        p=(x-v)*q-(x-w)*r; 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        q=2.0*(q-r); 
   for(h=1; h <=nhstepm; h++){        if (q > 0.0) p = -p; 
     for(d=1; d <=hstepm; d++){        q=fabs(q); 
       newm=savm;        etemp=e; 
       /* Covariates have to be included here again */        e=d; 
       cov[1]=1.;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        else { 
       for (k=1; k<=cptcovage;k++)          d=p/q; 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          u=x+d; 
       for (k=1; k<=cptcovprod;k++)          if (u-a < tol2 || b-u < tol2) 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];            d=SIGN(tol1,xm-x); 
         } 
       } else { 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       /*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,      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      fu=(*f)(u); 
       savm=oldm;      if (fu <= fx) { 
       oldm=newm;        if (u >= x) a=x; else b=x; 
     }        SHFT(v,w,x,u) 
     for(i=1; i<=nlstate+ndeath; i++)          SHFT(fv,fw,fx,fu) 
       for(j=1;j<=nlstate+ndeath;j++) {          } else { 
         po[i][j][h]=newm[i][j];            if (u < x) a=u; else b=u; 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);            if (fu <= fw || w == x) { 
          */              v=w; 
       }              w=u; 
   } /* end h */              fv=fw; 
   return po;              fw=fu; 
 }            } else if (fu <= fv || v == x || v == w) { 
               v=u; 
               fv=fu; 
 /*************** log-likelihood *************/            } 
 double func( double *x)          } 
 {    } 
   int i, ii, j, k, mi, d, kk;    nrerror("Too many iterations in brent"); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    *xmin=x; 
   double **out;    return fx; 
   double sw; /* Sum of weights */  } 
   double lli; /* Individual log likelihood */  
   long ipmx;  /****************** mnbrak ***********************/
   /*extern weight */  
   /* We are differentiating ll according to initial status */  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/              double (*func)(double)) 
   /*for(i=1;i<imx;i++)  { 
     printf(" %d\n",s[4][i]);    double ulim,u,r,q, dum;
   */    double fu; 
   cov[1]=1.;   
     *fa=(*func)(*ax); 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    *fb=(*func)(*bx); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    if (*fb > *fa) { 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      SHFT(dum,*ax,*bx,dum) 
     for(mi=1; mi<= wav[i]-1; mi++){        SHFT(dum,*fb,*fa,dum) 
       for (ii=1;ii<=nlstate+ndeath;ii++)        } 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    *cx=(*bx)+GOLD*(*bx-*ax); 
       for(d=0; d<dh[mi][i]; d++){    *fc=(*func)(*cx); 
         newm=savm;    while (*fb > *fc) { 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      r=(*bx-*ax)*(*fb-*fc); 
         for (kk=1; kk<=cptcovage;kk++) {      q=(*bx-*cx)*(*fb-*fa); 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
              ulim=(*bx)+GLIMIT*(*cx-*bx); 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      if ((*bx-u)*(u-*cx) > 0.0) { 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        fu=(*func)(u); 
         savm=oldm;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         oldm=newm;        fu=(*func)(u); 
                if (fu < *fc) { 
                  SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       } /* end mult */            SHFT(*fb,*fc,fu,(*func)(u)) 
                  } 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        u=ulim; 
       ipmx +=1;        fu=(*func)(u); 
       sw += weight[i];      } else { 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        u=(*cx)+GOLD*(*cx-*bx); 
     } /* end of wave */        fu=(*func)(u); 
   } /* end of individual */      } 
       SHFT(*ax,*bx,*cx,u) 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        SHFT(*fa,*fb,*fc,fu) 
   /* 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;  
 }  /*************** linmin ************************/
   
   int ncom; 
 /*********** Maximum Likelihood Estimation ***************/  double *pcom,*xicom;
   double (*nrfunc)(double []); 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))   
 {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   int i,j, iter;  { 
   double **xi,*delti;    double brent(double ax, double bx, double cx, 
   double fret;                 double (*f)(double), double tol, double *xmin); 
   xi=matrix(1,npar,1,npar);    double f1dim(double x); 
   for (i=1;i<=npar;i++)    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     for (j=1;j<=npar;j++)                double *fc, double (*func)(double)); 
       xi[i][j]=(i==j ? 1.0 : 0.0);    int j; 
   printf("Powell\n");    double xx,xmin,bx,ax; 
   powell(p,xi,npar,ftol,&iter,&fret,func);    double fx,fb,fa;
    
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    ncom=n; 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    pcom=vector(1,n); 
     xicom=vector(1,n); 
 }    nrfunc=func; 
     for (j=1;j<=n;j++) { 
 /**** Computes Hessian and covariance matrix ***/      pcom[j]=p[j]; 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      xicom[j]=xi[j]; 
 {    } 
   double  **a,**y,*x,pd;    ax=0.0; 
   double **hess;    xx=1.0; 
   int i, j,jk;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   int *indx;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   #ifdef DEBUG
   double hessii(double p[], double delta, int theta, double delti[]);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   double hessij(double p[], double delti[], int i, int j);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   void lubksb(double **a, int npar, int *indx, double b[]) ;  #endif
   void ludcmp(double **a, int npar, int *indx, double *d) ;    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
   hess=matrix(1,npar,1,npar);      p[j] += xi[j]; 
     } 
   printf("\nCalculation of the hessian matrix. Wait...\n");    free_vector(xicom,1,n); 
   for (i=1;i<=npar;i++){    free_vector(pcom,1,n); 
     printf("%d",i);fflush(stdout);  } 
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/  char *asc_diff_time(long time_sec, char ascdiff[])
     /*printf(" %lf ",hess[i][i]);*/  {
   }    long sec_left, days, hours, minutes;
      days = (time_sec) / (60*60*24);
   for (i=1;i<=npar;i++) {    sec_left = (time_sec) % (60*60*24);
     for (j=1;j<=npar;j++)  {    hours = (sec_left) / (60*60) ;
       if (j>i) {    sec_left = (sec_left) %(60*60);
         printf(".%d%d",i,j);fflush(stdout);    minutes = (sec_left) /60;
         hess[i][j]=hessij(p,delti,i,j);    sec_left = (sec_left) % (60);
         hess[j][i]=hess[i][j];        sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
         /*printf(" %lf ",hess[i][j]);*/    return ascdiff;
       }  }
     }  
   }  /*************** powell ************************/
   printf("\n");  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               double (*func)(double [])) 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  { 
      void linmin(double p[], double xi[], int n, double *fret, 
   a=matrix(1,npar,1,npar);                double (*func)(double [])); 
   y=matrix(1,npar,1,npar);    int i,ibig,j; 
   x=vector(1,npar);    double del,t,*pt,*ptt,*xit;
   indx=ivector(1,npar);    double fp,fptt;
   for (i=1;i<=npar;i++)    double *xits;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    int niterf, itmp;
   ludcmp(a,npar,indx,&pd);  
     pt=vector(1,n); 
   for (j=1;j<=npar;j++) {    ptt=vector(1,n); 
     for (i=1;i<=npar;i++) x[i]=0;    xit=vector(1,n); 
     x[j]=1;    xits=vector(1,n); 
     lubksb(a,npar,indx,x);    *fret=(*func)(p); 
     for (i=1;i<=npar;i++){    for (j=1;j<=n;j++) pt[j]=p[j]; 
       matcov[i][j]=x[i];    for (*iter=1;;++(*iter)) { 
     }      fp=(*fret); 
   }      ibig=0; 
       del=0.0; 
   printf("\n#Hessian matrix#\n");      last_time=curr_time;
   for (i=1;i<=npar;i++) {      (void) gettimeofday(&curr_time,&tzp);
     for (j=1;j<=npar;j++) {      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);
       printf("%.3e ",hess[i][j]);      /*    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);
     printf("\n");      */
   }     for (i=1;i<=n;i++) {
         printf(" %d %.12f",i, p[i]);
   /* Recompute Inverse */        fprintf(ficlog," %d %.12lf",i, p[i]);
   for (i=1;i<=npar;i++)        fprintf(ficrespow," %.12lf", p[i]);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      }
   ludcmp(a,npar,indx,&pd);      printf("\n");
       fprintf(ficlog,"\n");
   /*  printf("\n#Hessian matrix recomputed#\n");      fprintf(ficrespow,"\n");fflush(ficrespow);
       if(*iter <=3){
   for (j=1;j<=npar;j++) {        tm = *localtime(&curr_time.tv_sec);
     for (i=1;i<=npar;i++) x[i]=0;        strcpy(strcurr,asctime(&tm));
     x[j]=1;  /*       asctime_r(&tm,strcurr); */
     lubksb(a,npar,indx,x);        forecast_time=curr_time; 
     for (i=1;i<=npar;i++){        itmp = strlen(strcurr);
       y[i][j]=x[i];        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
       printf("%.3e ",y[i][j]);          strcurr[itmp-1]='\0';
     }        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     printf("\n");        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   }        for(niterf=10;niterf<=30;niterf+=10){
   */          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
           tmf = *localtime(&forecast_time.tv_sec);
   free_matrix(a,1,npar,1,npar);  /*      asctime_r(&tmf,strfor); */
   free_matrix(y,1,npar,1,npar);          strcpy(strfor,asctime(&tmf));
   free_vector(x,1,npar);          itmp = strlen(strfor);
   free_ivector(indx,1,npar);          if(strfor[itmp-1]=='\n')
   free_matrix(hess,1,npar,1,npar);          strfor[itmp-1]='\0';
           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);
 }        }
       }
 /*************** hessian matrix ****************/      for (i=1;i<=n;i++) { 
 double hessii( double x[], double delta, int theta, double delti[])        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
 {        fptt=(*fret); 
   int i;  #ifdef DEBUG
   int l=1, lmax=20;        printf("fret=%lf \n",*fret);
   double k1,k2;        fprintf(ficlog,"fret=%lf \n",*fret);
   double p2[NPARMAX+1];  #endif
   double res;        printf("%d",i);fflush(stdout);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        fprintf(ficlog,"%d",i);fflush(ficlog);
   double fx;        linmin(p,xit,n,fret,func); 
   int k=0,kmax=10;        if (fabs(fptt-(*fret)) > del) { 
   double l1;          del=fabs(fptt-(*fret)); 
           ibig=i; 
   fx=func(x);        } 
   for (i=1;i<=npar;i++) p2[i]=x[i];  #ifdef DEBUG
   for(l=0 ; l <=lmax; l++){        printf("%d %.12e",i,(*fret));
     l1=pow(10,l);        fprintf(ficlog,"%d %.12e",i,(*fret));
     delts=delt;        for (j=1;j<=n;j++) {
     for(k=1 ; k <kmax; k=k+1){          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       delt = delta*(l1*k);          printf(" x(%d)=%.12e",j,xit[j]);
       p2[theta]=x[theta] +delt;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       k1=func(p2)-fx;        }
       p2[theta]=x[theta]-delt;        for(j=1;j<=n;j++) {
       k2=func(p2)-fx;          printf(" p=%.12e",p[j]);
       /*res= (k1-2.0*fx+k2)/delt/delt; */          fprintf(ficlog," p=%.12e",p[j]);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        }
              printf("\n");
 #ifdef DEBUG        fprintf(ficlog,"\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);  #endif
 #endif      } 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  #ifdef DEBUG
         k=kmax;        int k[2],l;
       }        k[0]=1;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        k[1]=-1;
         k=kmax; l=lmax*10.;        printf("Max: %.12e",(*func)(p));
       }        fprintf(ficlog,"Max: %.12e",(*func)(p));
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        for (j=1;j<=n;j++) {
         delts=delt;          printf(" %.12e",p[j]);
       }          fprintf(ficlog," %.12e",p[j]);
     }        }
   }        printf("\n");
   delti[theta]=delts;        fprintf(ficlog,"\n");
   return res;        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]);
 double hessij( double x[], double delti[], int thetai,int thetaj)            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 {          }
   int i;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   int l=1, l1, lmax=20;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double k1,k2,k3,k4,res,fx;        }
   double p2[NPARMAX+1];  #endif
   int k;  
   
   fx=func(x);        free_vector(xit,1,n); 
   for (k=1; k<=2; k++) {        free_vector(xits,1,n); 
     for (i=1;i<=npar;i++) p2[i]=x[i];        free_vector(ptt,1,n); 
     p2[thetai]=x[thetai]+delti[thetai]/k;        free_vector(pt,1,n); 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        return; 
     k1=func(p2)-fx;      } 
        if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     p2[thetai]=x[thetai]+delti[thetai]/k;      for (j=1;j<=n;j++) { 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        ptt[j]=2.0*p[j]-pt[j]; 
     k2=func(p2)-fx;        xit[j]=p[j]-pt[j]; 
          pt[j]=p[j]; 
     p2[thetai]=x[thetai]-delti[thetai]/k;      } 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      fptt=(*func)(ptt); 
     k3=func(p2)-fx;      if (fptt < fp) { 
          t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     p2[thetai]=x[thetai]-delti[thetai]/k;        if (t < 0.0) { 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          linmin(p,xit,n,fret,func); 
     k4=func(p2)-fx;          for (j=1;j<=n;j++) { 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */            xi[j][ibig]=xi[j][n]; 
 #ifdef DEBUG            xi[j][n]=xit[j]; 
     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);          }
 #endif  #ifdef DEBUG
   }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   return res;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 }          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
 /************** Inverse of matrix **************/            fprintf(ficlog," %.12e",xit[j]);
 void ludcmp(double **a, int n, int *indx, double *d)          }
 {          printf("\n");
   int i,imax,j,k;          fprintf(ficlog,"\n");
   double big,dum,sum,temp;  #endif
   double *vv;        }
        } 
   vv=vector(1,n);    } 
   *d=1.0;  } 
   for (i=1;i<=n;i++) {  
     big=0.0;  /**** Prevalence limit (stable or period prevalence)  ****************/
     for (j=1;j<=n;j++)  
       if ((temp=fabs(a[i][j])) > big) big=temp;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  {
     vv[i]=1.0/big;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   }       matrix by transitions matrix until convergence is reached */
   for (j=1;j<=n;j++) {  
     for (i=1;i<j;i++) {    int i, ii,j,k;
       sum=a[i][j];    double min, max, maxmin, maxmax,sumnew=0.;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    double **matprod2();
       a[i][j]=sum;    double **out, cov[NCOVMAX], **pmij();
     }    double **newm;
     big=0.0;    double agefin, delaymax=50 ; /* Max number of years to converge */
     for (i=j;i<=n;i++) {  
       sum=a[i][j];    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (k=1;k<j;k++)      for (j=1;j<=nlstate+ndeath;j++){
         sum -= a[i][k]*a[k][j];        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       a[i][j]=sum;      }
       if ( (dum=vv[i]*fabs(sum)) >= big) {  
         big=dum;     cov[1]=1.;
         imax=i;   
       }   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     }    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     if (j != imax) {      newm=savm;
       for (k=1;k<=n;k++) {      /* Covariates have to be included here again */
         dum=a[imax][k];       cov[2]=agefin;
         a[imax][k]=a[j][k];    
         a[j][k]=dum;        for (k=1; k<=cptcovn;k++) {
       }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       *d = -(*d);          /*      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]]);*/
       vv[imax]=vv[j];        }
     }        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     indx[j]=imax;        for (k=1; k<=cptcovprod;k++)
     if (a[j][j] == 0.0) a[j][j]=TINY;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     if (j != n) {  
       dum=1.0/(a[j][j]);        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     }        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   }      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   free_vector(vv,1,n);  /* Doesn't work */  
 ;      savm=oldm;
 }      oldm=newm;
       maxmax=0.;
 void lubksb(double **a, int n, int *indx, double b[])      for(j=1;j<=nlstate;j++){
 {        min=1.;
   int i,ii=0,ip,j;        max=0.;
   double sum;        for(i=1; i<=nlstate; i++) {
            sumnew=0;
   for (i=1;i<=n;i++) {          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     ip=indx[i];          prlim[i][j]= newm[i][j]/(1-sumnew);
     sum=b[ip];          max=FMAX(max,prlim[i][j]);
     b[ip]=b[i];          min=FMIN(min,prlim[i][j]);
     if (ii)        }
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        maxmin=max-min;
     else if (sum) ii=i;        maxmax=FMAX(maxmax,maxmin);
     b[i]=sum;      }
   }      if(maxmax < ftolpl){
   for (i=n;i>=1;i--) {        return prlim;
     sum=b[i];      }
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    }
     b[i]=sum/a[i][i];  }
   }  
 }  /*************** transition probabilities ***************/ 
   
 /************ Frequencies ********************/  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 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 */    double s1, s2;
      /*double t34;*/
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    int i,j,j1, nc, ii, jj;
   double ***freq; /* Frequencies */  
   double *pp;      for(i=1; i<= nlstate; i++){
   double pos, k2, dateintsum=0,k2cpt=0;        for(j=1; j<i;j++){
   FILE *ficresp;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   char fileresp[FILENAMELENGTH];            /*s2 += param[i][j][nc]*cov[nc];*/
              s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   pp=vector(1,nlstate);  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
   strcpy(fileresp,"p");          ps[i][j]=s2;
   strcat(fileresp,fileres);  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   if((ficresp=fopen(fileresp,"w"))==NULL) {        }
     printf("Problem with prevalence resultfile: %s\n", fileresp);        for(j=i+1; j<=nlstate+ndeath;j++){
     exit(0);          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];
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
   j1=0;          }
            ps[i][j]=s2;
   j=cptcoveff;        }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      }
        /*ps[3][2]=1;*/
   for(k1=1; k1<=j;k1++){      
     for(i1=1; i1<=ncodemax[k1];i1++){      for(i=1; i<= nlstate; i++){
       j1++;        s1=0;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        for(j=1; j<i; j++)
         scanf("%d", i);*/          s1+=exp(ps[i][j]);
       for (i=-1; i<=nlstate+ndeath; i++)          for(j=i+1; j<=nlstate+ndeath; j++)
         for (jk=-1; jk<=nlstate+ndeath; jk++)            s1+=exp(ps[i][j]);
           for(m=agemin; m <= agemax+3; m++)        ps[i][i]=1./(s1+1.);
             freq[i][jk][m]=0;        for(j=1; j<i; j++)
                ps[i][j]= exp(ps[i][j])*ps[i][i];
       dateintsum=0;        for(j=i+1; j<=nlstate+ndeath; j++)
       k2cpt=0;          ps[i][j]= exp(ps[i][j])*ps[i][i];
       for (i=1; i<=imx; i++) {        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         bool=1;      } /* end i */
         if  (cptcovn>0) {      
           for (z1=1; z1<=cptcoveff; z1++)      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        for(jj=1; jj<= nlstate+ndeath; jj++){
               bool=0;          ps[ii][jj]=0;
         }          ps[ii][ii]=1;
         if (bool==1) {        }
           for(m=firstpass; m<=lastpass; m++){      }
             k2=anint[m][i]+(mint[m][i]/12.);      
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  
               if(agev[m][i]==0) agev[m][i]=agemax+1;  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
               if(agev[m][i]==1) agev[m][i]=agemax+2;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
               if (m<lastpass) {  /*         printf("ddd %lf ",ps[ii][jj]); */
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  /*       } */
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  /*       printf("\n "); */
               }  /*        } */
                /*        printf("\n ");printf("%lf ",cov[2]); */
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {         /*
                 dateintsum=dateintsum+k2;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
                 k2cpt++;        goto end;*/
               }      return ps;
             }  }
           }  
         }  /**************** Product of 2 matrices ******************/
       }  
          double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       if  (cptcovn>0) {       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
         fprintf(ficresp, "\n#********** Variable ");    /* in, b, out are matrice of pointers which should have been initialized 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);       before: only the contents of out is modified. The function returns
         fprintf(ficresp, "**********\n#");       a pointer to pointers identical to out */
       }    long i, j, k;
       for(i=1; i<=nlstate;i++)    for(i=nrl; i<= nrh; i++)
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      for(k=ncolol; k<=ncoloh; k++)
       fprintf(ficresp, "\n");        for(j=ncl,out[i][k]=0.; j<=nch; j++)
                out[i][k] +=in[i][j]*b[j][k];
       for(i=(int)agemin; i <= (int)agemax+3; i++){  
         if(i==(int)agemax+3)    return out;
           printf("Total");  }
         else  
           printf("Age %d", i);  
         for(jk=1; jk <=nlstate ; jk++){  /************* Higher Matrix Product ***************/
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  
             pp[jk] += freq[jk][m][i];  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         }  {
         for(jk=1; jk <=nlstate ; jk++){    /* Computes the transition matrix starting at age 'age' over 
           for(m=-1, pos=0; m <=0 ; m++)       'nhstepm*hstepm*stepm' months (i.e. until
             pos += freq[jk][m][i];       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
           if(pp[jk]>=1.e-10)       nhstepm*hstepm matrices. 
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
           else       (typically every 2 years instead of every month which is too big 
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);       for the memory).
         }       Model is determined by parameters x and covariates have to be 
        included manually here. 
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)       */
             pp[jk] += freq[jk][m][i];  
         }    int i, j, d, h, k;
     double **out, cov[NCOVMAX];
         for(jk=1,pos=0; jk <=nlstate ; jk++)    double **newm;
           pos += pp[jk];  
         for(jk=1; jk <=nlstate ; jk++){    /* Hstepm could be zero and should return the unit matrix */
           if(pos>=1.e-5)    for (i=1;i<=nlstate+ndeath;i++)
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      for (j=1;j<=nlstate+ndeath;j++){
           else        oldm[i][j]=(i==j ? 1.0 : 0.0);
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        po[i][j][0]=(i==j ? 1.0 : 0.0);
           if( i <= (int) agemax){      }
             if(pos>=1.e-5){    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    for(h=1; h <=nhstepm; h++){
               probs[i][jk][j1]= pp[jk]/pos;      for(d=1; d <=hstepm; d++){
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        newm=savm;
             }        /* Covariates have to be included here again */
             else        cov[1]=1.;
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
           }        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         }        for (k=1; k<=cptcovage;k++)
                  cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for(jk=-1; jk <=nlstate+ndeath; jk++)        for (k=1; k<=cptcovprod;k++)
           for(m=-1; m <=nlstate+ndeath; m++)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  
         if(i <= (int) agemax)  
           fprintf(ficresp,"\n");        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         printf("\n");        /*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;
   dateintmean=dateintsum/k2cpt;        oldm=newm;
        }
   fclose(ficresp);      for(i=1; i<=nlstate+ndeath; i++)
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        for(j=1;j<=nlstate+ndeath;j++) {
   free_vector(pp,1,nlstate);          po[i][j][h]=newm[i][j];
            /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   /* End of Freq */           */
 }        }
     } /* end h */
 /************ Prevalence ********************/    return po;
 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)  }
 {  /* Some frequencies */  
    
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  /*************** log-likelihood *************/
   double ***freq; /* Frequencies */  double func( double *x)
   double *pp;  {
   double pos, k2;    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
   pp=vector(1,nlstate);    double **out;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    double sw; /* Sum of weights */
      double lli; /* Individual log likelihood */
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    int s1, s2;
   j1=0;    double bbh, survp;
      long ipmx;
   j=cptcoveff;    /*extern weight */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    /* We are differentiating ll according to initial status */
      /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   for(k1=1; k1<=j;k1++){    /*for(i=1;i<imx;i++) 
     for(i1=1; i1<=ncodemax[k1];i1++){      printf(" %d\n",s[4][i]);
       j1++;    */
          cov[1]=1.;
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)      for(k=1; k<=nlstate; k++) ll[k]=0.;
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;    if(mle==1){
            for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (i=1; i<=imx; i++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         bool=1;        for(mi=1; mi<= wav[i]-1; mi++){
         if  (cptcovn>0) {          for (ii=1;ii<=nlstate+ndeath;ii++)
           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[ii][j]=(ii==j ? 1.0 : 0.0);
               bool=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            }
         if (bool==1) {          for(d=0; d<dh[mi][i]; d++){
           for(m=firstpass; m<=lastpass; m++){            newm=savm;
             k2=anint[m][i]+(mint[m][i]/12.);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            for (kk=1; kk<=cptcovage;kk++) {
               if(agev[m][i]==0) agev[m][i]=agemax+1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
               if(agev[m][i]==1) agev[m][i]=agemax+2;            }
               if (m<lastpass) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                 if (calagedate>0)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];            savm=oldm;
                 else            oldm=newm;
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          } /* end mult */
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];        
               }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
             }          /* But now since version 0.9 we anticipate for bias at large stepm.
           }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         }           * (in months) between two waves is not a multiple of stepm, we rounded to 
       }           * the nearest (and in case of equal distance, to the lowest) interval but now
       for(i=(int)agemin; i <= (int)agemax+3; i++){           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         for(jk=1; jk <=nlstate ; jk++){           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)           * probability in order to take into account the bias as a fraction of the way
             pp[jk] += freq[jk][m][i];           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
         }           * -stepm/2 to stepm/2 .
         for(jk=1; jk <=nlstate ; jk++){           * For stepm=1 the results are the same as for previous versions of Imach.
           for(m=-1, pos=0; m <=0 ; m++)           * For stepm > 1 the results are less biased than in previous versions. 
             pos += freq[jk][m][i];           */
         }          s1=s[mw[mi][i]][i];
                  s2=s[mw[mi+1][i]][i];
         for(jk=1; jk <=nlstate ; jk++){          bbh=(double)bh[mi][i]/(double)stepm; 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          /* bias bh is positive if real duration
             pp[jk] += freq[jk][m][i];           * is higher than the multiple of stepm and negative otherwise.
         }           */
                  /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          if( s2 > nlstate){ 
                    /* i.e. if s2 is a death state and if the date of death is known 
         for(jk=1; jk <=nlstate ; jk++){                   then the contribution to the likelihood is the probability to 
           if( i <= (int) agemax){               die between last step unit time and current  step unit time, 
             if(pos>=1.e-5){               which is also equal to probability to die before dh 
               probs[i][jk][j1]= pp[jk]/pos;               minus probability to die before dh-stepm . 
             }               In version up to 0.92 likelihood was computed
           }          as if date of death was unknown. Death was treated as any other
         }          health state: the date of the interview describes the actual state
                  and not the date of a change in health state. The former idea was
       }          to consider that at each interview the state was recorded
     }          (healthy, disable or death) and IMaCh was corrected; but when we
   }          introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
            contribution is smaller and very dependent of the step unit
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          stepm. It is no more the probability to die between last interview
   free_vector(pp,1,nlstate);          and month of death but the probability to survive from last
            interview up to one month before death multiplied by the
 }  /* End of Freq */          probability to die within a month. Thanks to Chris
           Jackson for correcting this bug.  Former versions increased
 /************* Waves Concatenation ***************/          mortality artificially. The bad side is that we add another loop
           which slows down the processing. The difference can be up to 10%
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          lower mortality.
 {            */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.            lli=log(out[s1][s2] - savm[s1][s2]);
      Death is a valid wave (if date is known).  
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          } else if  (s2==-2) {
      and mw[mi+1][i]. dh depends on stepm.            for (j=1,survp=0. ; j<=nlstate; j++) 
      */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             /*survp += out[s1][j]; */
   int i, mi, m;            lli= log(survp);
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          }
      double sum=0., jmean=0.;*/          
           else if  (s2==-4) { 
   int j, k=0,jk, ju, jl;            for (j=3,survp=0. ; j<=nlstate; j++)  
   double sum=0.;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   jmin=1e+5;            lli= log(survp); 
   jmax=-1;          } 
   jmean=0.;  
   for(i=1; i<=imx; i++){          else if  (s2==-5) { 
     mi=0;            for (j=1,survp=0. ; j<=2; j++)  
     m=firstpass;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     while(s[m][i] <= nlstate){            lli= log(survp); 
       if(s[m][i]>=1)          } 
         mw[++mi][i]=m;          
       if(m >=lastpass)          else{
         break;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       else            /*  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 */
         m++;          } 
     }/* end while */          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     if (s[m][i] > nlstate){          /*if(lli ==000.0)*/
       mi++;     /* Death is another wave */          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       /* if(mi==0)  never been interviewed correctly before death */          ipmx +=1;
          /* Only death is a correct wave */          sw += weight[i];
       mw[mi][i]=m;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
       } /* end of individual */
     wav[i]=mi;    }  else if(mle==2){
     if(mi==0)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   for(i=1; i<=imx; i++){            for (j=1;j<=nlstate+ndeath;j++){
     for(mi=1; mi<wav[i];mi++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       if (stepm <=0)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         dh[mi][i]=1;            }
       else{          for(d=0; d<=dh[mi][i]; d++){
         if (s[mw[mi+1][i]][i] > nlstate) {            newm=savm;
           if (agedc[i] < 2*AGESUP) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);            for (kk=1; kk<=cptcovage;kk++) {
           if(j==0) j=1;  /* Survives at least one month after exam */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           k=k+1;            }
           if (j >= jmax) jmax=j;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           if (j <= jmin) jmin=j;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           sum=sum+j;            savm=oldm;
           /*if (j<0) printf("j=%d num=%d \n",j,i); */            oldm=newm;
           }          } /* end mult */
         }        
         else{          s1=s[mw[mi][i]][i];
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          s2=s[mw[mi+1][i]][i];
           k=k+1;          bbh=(double)bh[mi][i]/(double)stepm; 
           if (j >= jmax) jmax=j;          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 (j <= jmin)jmin=j;          ipmx +=1;
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          sw += weight[i];
           sum=sum+j;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         }        } /* end of wave */
         jk= j/stepm;      } /* end of individual */
         jl= j -jk*stepm;    }  else if(mle==3){  /* exponential inter-extrapolation */
         ju= j -(jk+1)*stepm;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         if(jl <= -ju)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           dh[mi][i]=jk;        for(mi=1; mi<= wav[i]-1; mi++){
         else          for (ii=1;ii<=nlstate+ndeath;ii++)
           dh[mi][i]=jk+1;            for (j=1;j<=nlstate+ndeath;j++){
         if(dh[mi][i]==0)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           dh[mi][i]=1; /* At least one step */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
     }          for(d=0; d<dh[mi][i]; d++){
   }            newm=savm;
   jmean=sum/k;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            for (kk=1; kk<=cptcovage;kk++) {
  }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 /*********** Tricode ****************************/            }
 void tricode(int *Tvar, int **nbcode, int imx)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int Ndum[20],ij=1, k, j, i;            savm=oldm;
   int cptcode=0;            oldm=newm;
   cptcoveff=0;          } /* end mult */
          
   for (k=0; k<19; k++) Ndum[k]=0;          s1=s[mw[mi][i]][i];
   for (k=1; k<=7; k++) ncodemax[k]=0;          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     for (i=1; i<=imx; i++) {          ipmx +=1;
       ij=(int)(covar[Tvar[j]][i]);          sw += weight[i];
       Ndum[ij]++;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/        } /* end of wave */
       if (ij > cptcode) cptcode=ij;      } /* end of individual */
     }    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       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;
  for (k=0; k<19; k++) Ndum[k]=0;          } /* end mult */
         
  for (i=1; i<=ncovmodel-2; i++) {          s1=s[mw[mi][i]][i];
       ij=Tvar[i];          s2=s[mw[mi+1][i]][i];
       Ndum[ij]++;          if( s2 > nlstate){ 
     }            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
  ij=1;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
  for (i=1; i<=10; i++) {          }
    if((Ndum[i]!=0) && (i<=ncovcol)){          ipmx +=1;
      Tvaraff[ij]=i;          sw += weight[i];
      ij++;          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 of wave */
        } /* end of individual */
     cptcoveff=ij-1;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
 }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 /*********** Health Expectancies ****************/        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
 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 )            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);
   /* Health expectancies */            }
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;          for(d=0; d<dh[mi][i]; d++){
   double age, agelim, hf;            newm=savm;
   double ***p3mat,***varhe;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double **dnewm,**doldm;            for (kk=1; kk<=cptcovage;kk++) {
   double *xp;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double **gp, **gm;            }
   double ***gradg, ***trgradg;          
   int theta;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);            savm=oldm;
   xp=vector(1,npar);            oldm=newm;
   dnewm=matrix(1,nlstate*2,1,npar);          } /* end mult */
   doldm=matrix(1,nlstate*2,1,nlstate*2);        
            s1=s[mw[mi][i]][i];
   fprintf(ficreseij,"# Health expectancies\n");          s2=s[mw[mi+1][i]][i];
   fprintf(ficreseij,"# Age");          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   for(i=1; i<=nlstate;i++)          ipmx +=1;
     for(j=1; j<=nlstate;j++)          sw += weight[i];
       fprintf(ficreseij," %1d-%1d (SE)",i,j);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   fprintf(ficreseij,"\n");          /*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 of wave */
   if(estepm < stepm){      } /* end of individual */
     printf ("Problem %d lower than %d\n",estepm, stepm);    } /* End of if */
   }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   else  hstepm=estepm;      /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   /* We compute the life expectancy from trapezoids spaced every estepm months    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
    * This is mainly to measure the difference between two models: for example    return -l;
    * 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  
    * progression inbetween and thus overestimating or underestimating according  /*************** log-likelihood *************/
    * to the curvature of the survival function. If, for the same date, we  double funcone( double *x)
    * estimate the model with stepm=1 month, we can keep estepm to 24 months  {
    * to compare the new estimate of Life expectancy with the same linear    /* Same as likeli but slower because of a lot of printf and if */
    * hypothesis. A more precise result, taking into account a more precise    int i, ii, j, k, mi, d, kk;
    * curvature will be obtained if estepm is as small as stepm. */    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
   /* For example we decided to compute the life expectancy with the smallest unit */    double lli; /* Individual log likelihood */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    double llt;
      nhstepm is the number of hstepm from age to agelim    int s1, s2;
      nstepm is the number of stepm from age to agelin.    double bbh, survp;
      Look at hpijx to understand the reason of that which relies in memory size    /*extern weight */
      and note for a fixed period like estepm months */    /* We are differentiating ll according to initial status */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      survival function given by stepm (the optimization length). Unfortunately it    /*for(i=1;i<imx;i++) 
      means that if the survival funtion is printed only each two years of age and if      printf(" %d\n",s[4][i]);
      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.    cov[1]=1.;
   */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
   agelim=AGESUP;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     /* nhstepm age range expressed in number of stepm */      for(mi=1; mi<= wav[i]-1; mi++){
     nstepm=(int) rint((agelim-age)*YEARM/stepm);        for (ii=1;ii<=nlstate+ndeath;ii++)
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */          for (j=1;j<=nlstate+ndeath;j++){
     /* if (stepm >= YEARM) hstepm=1;*/            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);        for(d=0; d<dh[mi][i]; d++){
     gp=matrix(0,nhstepm,1,nlstate*2);          newm=savm;
     gm=matrix(0,nhstepm,1,nlstate*2);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          }
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          oldm=newm;
         } /* end mult */
     /* Computing Variances of health expectancies */        
         s1=s[mw[mi][i]][i];
      for(theta=1; theta <=npar; theta++){        s2=s[mw[mi+1][i]][i];
       for(i=1; i<=npar; i++){        bbh=(double)bh[mi][i]/(double)stepm; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        /* bias is positive if real duration
       }         * is higher than the multiple of stepm and negative otherwise.
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);           */
          if( s2 > nlstate && (mle <5) ){  /* Jackson */
       cptj=0;          lli=log(out[s1][s2] - savm[s1][s2]);
       for(j=1; j<= nlstate; j++){        } else if  (s2==-2) {
         for(i=1; i<=nlstate; i++){          for (j=1,survp=0. ; j<=nlstate; j++) 
           cptj=cptj+1;            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){          lli= log(survp);
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        }else if (mle==1){
           }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         }        } else if(mle==2){
       }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
              } else if(mle==3){  /* exponential inter-extrapolation */
                lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       for(i=1; i<=npar; i++)        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          lli=log(out[s1][s2]); /* Original formula */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
                lli=log(out[s1][s2]); /* Original formula */
       cptj=0;        } /* End of if */
       for(j=1; j<= nlstate; j++){        ipmx +=1;
         for(i=1;i<=nlstate;i++){        sw += weight[i];
           cptj=cptj+1;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){  /*       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]); */
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;        if(globpr){
           }          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
         }   %11.6f %11.6f %11.6f ", \
       }                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       for(j=1; j<= nlstate*2; j++)                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         for(h=0; h<=nhstepm-1; h++){          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            llt +=ll[k]*gipmx/gsw;
         }            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
      }          }
              fprintf(ficresilk," %10.6f\n", -llt);
 /* End theta */        }
       } /* end of wave */
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
      for(h=0; h<=nhstepm-1; h++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       for(j=1; j<=nlstate*2;j++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         for(theta=1; theta <=npar; theta++)    if(globpr==0){ /* First time we count the contributions and weights */
           trgradg[h][j][theta]=gradg[h][theta][j];      gipmx=ipmx;
            gsw=sw;
     }
      for(i=1;i<=nlstate*2;i++)    return -l;
       for(j=1;j<=nlstate*2;j++)  }
         varhe[i][j][(int)age] =0.;  
   
      printf("%d|",(int)age);fflush(stdout);  /*************** function likelione ***********/
      for(h=0;h<=nhstepm-1;h++){  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
       for(k=0;k<=nhstepm-1;k++){  {
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    /* This routine should help understanding what is done with 
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);       the selection of individuals/waves and
         for(i=1;i<=nlstate*2;i++)       to check the exact contribution to the likelihood.
           for(j=1;j<=nlstate*2;j++)       Plotting could be done.
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;     */
       }    int k;
     }  
     if(*globpri !=0){ /* Just counts and sums, no printings */
            strcpy(fileresilk,"ilk"); 
     /* Computing expectancies */      strcat(fileresilk,fileres);
     for(i=1; i<=nlstate;i++)      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       for(j=1; j<=nlstate;j++)        printf("Problem with resultfile: %s\n", fileresilk);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      }
                fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
 /* if((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(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
         }      for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     fprintf(ficreseij,"%3.0f",age );      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     cptj=0;    }
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){    *fretone=(*funcone)(p);
         cptj++;    if(*globpri !=0){
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      fclose(ficresilk);
       }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     fprintf(ficreseij,"\n");      fflush(fichtm); 
        } 
     free_matrix(gm,0,nhstepm,1,nlstate*2);    return;
     free_matrix(gp,0,nhstepm,1,nlstate*2);  }
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*********** Maximum Likelihood Estimation ***************/
   }  
   free_vector(xp,1,npar);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   free_matrix(dnewm,1,nlstate*2,1,npar);  {
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);    int i,j, iter;
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);    double **xi;
 }    double fret;
     double fretone; /* Only one call to likelihood */
 /************ Variance ******************/    /*  char filerespow[FILENAMELENGTH];*/
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)    xi=matrix(1,npar,1,npar);
 {    for (i=1;i<=npar;i++)
   /* Variance of health expectancies */      for (j=1;j<=npar;j++)
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        xi[i][j]=(i==j ? 1.0 : 0.0);
   double **newm;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   double **dnewm,**doldm;    strcpy(filerespow,"pow"); 
   int i, j, nhstepm, hstepm, h, nstepm ;    strcat(filerespow,fileres);
   int k, cptcode;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   double *xp;      printf("Problem with resultfile: %s\n", filerespow);
   double **gp, **gm;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   double ***gradg, ***trgradg;    }
   double ***p3mat;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   double age,agelim, hf;    for (i=1;i<=nlstate;i++)
   int theta;      for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");    fprintf(ficrespow,"\n");
   fprintf(ficresvij,"# Age");  
   for(i=1; i<=nlstate;i++)    powell(p,xi,npar,ftol,&iter,&fret,func);
     for(j=1; j<=nlstate;j++)  
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    free_matrix(xi,1,npar,1,npar);
   fprintf(ficresvij,"\n");    fclose(ficrespow);
     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   xp=vector(1,npar);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   dnewm=matrix(1,nlstate,1,npar);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   doldm=matrix(1,nlstate,1,nlstate);  
    }
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);  /**** Computes Hessian and covariance matrix ***/
   }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   else  hstepm=estepm;    {
   /* For example we decided to compute the life expectancy with the smallest unit */    double  **a,**y,*x,pd;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    double **hess;
      nhstepm is the number of hstepm from age to agelim    int i, j,jk;
      nstepm is the number of stepm from age to agelin.    int *indx;
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like k years */    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
      survival function given by stepm (the optimization length). Unfortunately it    void lubksb(double **a, int npar, int *indx, double b[]) ;
      means that if the survival funtion is printed only each two years of age and if    void ludcmp(double **a, int npar, int *indx, double *d) ;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    double gompertz(double p[]);
      results. So we changed our mind and took the option of the best precision.    hess=matrix(1,npar,1,npar);
   */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    printf("\nCalculation of the hessian matrix. Wait...\n");
   agelim = AGESUP;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    for (i=1;i<=npar;i++){
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      printf("%d",i);fflush(stdout);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      fprintf(ficlog,"%d",i);fflush(ficlog);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     gp=matrix(0,nhstepm,1,nlstate);      
     gm=matrix(0,nhstepm,1,nlstate);      /*  printf(" %f ",p[i]);
           printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     for(theta=1; theta <=npar; theta++){    }
       for(i=1; i<=npar; i++){ /* Computes gradient */    
         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);          if (j>i) { 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          printf(".%d%d",i,j);fflush(stdout);
           fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       if (popbased==1) {          hess[i][j]=hessij(p,delti,i,j,func,npar);
         for(i=1; i<=nlstate;i++)          
           prlim[i][i]=probs[(int)age][i][ij];          hess[j][i]=hess[i][j];    
       }          /*printf(" %lf ",hess[i][j]);*/
          }
       for(j=1; j<= nlstate; j++){      }
         for(h=0; h<=nhstepm; h++){    }
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    printf("\n");
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    fprintf(ficlog,"\n");
         }  
       }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
        fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       for(i=1; i<=npar; i++) /* Computes gradient */    
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    a=matrix(1,npar,1,npar);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      y=matrix(1,npar,1,npar);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    x=vector(1,npar);
      indx=ivector(1,npar);
       if (popbased==1) {    for (i=1;i<=npar;i++)
         for(i=1; i<=nlstate;i++)      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
           prlim[i][i]=probs[(int)age][i][ij];    ludcmp(a,npar,indx,&pd);
       }  
     for (j=1;j<=npar;j++) {
       for(j=1; j<= nlstate; j++){      for (i=1;i<=npar;i++) x[i]=0;
         for(h=0; h<=nhstepm; h++){      x[j]=1;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      lubksb(a,npar,indx,x);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      for (i=1;i<=npar;i++){ 
         }        matcov[i][j]=x[i];
       }      }
     }
       for(j=1; j<= nlstate; j++)  
         for(h=0; h<=nhstepm; h++){    printf("\n#Hessian matrix#\n");
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    fprintf(ficlog,"\n#Hessian matrix#\n");
         }    for (i=1;i<=npar;i++) { 
     } /* End theta */      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        fprintf(ficlog,"%.3e ",hess[i][j]);
       }
     for(h=0; h<=nhstepm; h++)      printf("\n");
       for(j=1; j<=nlstate;j++)      fprintf(ficlog,"\n");
         for(theta=1; theta <=npar; theta++)    }
           trgradg[h][j][theta]=gradg[h][theta][j];  
     /* Recompute Inverse */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    for (i=1;i<=npar;i++)
     for(i=1;i<=nlstate;i++)      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       for(j=1;j<=nlstate;j++)    ludcmp(a,npar,indx,&pd);
         vareij[i][j][(int)age] =0.;  
     /*  printf("\n#Hessian matrix recomputed#\n");
     for(h=0;h<=nhstepm;h++){  
       for(k=0;k<=nhstepm;k++){    for (j=1;j<=npar;j++) {
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      for (i=1;i<=npar;i++) x[i]=0;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      x[j]=1;
         for(i=1;i<=nlstate;i++)      lubksb(a,npar,indx,x);
           for(j=1;j<=nlstate;j++)      for (i=1;i<=npar;i++){ 
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;        y[i][j]=x[i];
       }        printf("%.3e ",y[i][j]);
     }        fprintf(ficlog,"%.3e ",y[i][j]);
       }
     fprintf(ficresvij,"%.0f ",age );      printf("\n");
     for(i=1; i<=nlstate;i++)      fprintf(ficlog,"\n");
       for(j=1; j<=nlstate;j++){    }
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    */
       }  
     fprintf(ficresvij,"\n");    free_matrix(a,1,npar,1,npar);
     free_matrix(gp,0,nhstepm,1,nlstate);    free_matrix(y,1,npar,1,npar);
     free_matrix(gm,0,nhstepm,1,nlstate);    free_vector(x,1,npar);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    free_ivector(indx,1,npar);
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    free_matrix(hess,1,npar,1,npar);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */  
    }
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);  /*************** hessian matrix ****************/
   free_matrix(dnewm,1,nlstate,1,nlstate);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   {
 }    int i;
     int l=1, lmax=20;
 /************ Variance of prevlim ******************/    double k1,k2;
 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)    double p2[NPARMAX+1];
 {    double res;
   /* Variance of prevalence limit */    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    double fx;
   double **newm;    int k=0,kmax=10;
   double **dnewm,**doldm;    double l1;
   int i, j, nhstepm, hstepm;  
   int k, cptcode;    fx=func(x);
   double *xp;    for (i=1;i<=npar;i++) p2[i]=x[i];
   double *gp, *gm;    for(l=0 ; l <=lmax; l++){
   double **gradg, **trgradg;      l1=pow(10,l);
   double age,agelim;      delts=delt;
   int theta;      for(k=1 ; k <kmax; k=k+1){
            delt = delta*(l1*k);
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");        p2[theta]=x[theta] +delt;
   fprintf(ficresvpl,"# Age");        k1=func(p2)-fx;
   for(i=1; i<=nlstate;i++)        p2[theta]=x[theta]-delt;
       fprintf(ficresvpl," %1d-%1d",i,i);        k2=func(p2)-fx;
   fprintf(ficresvpl,"\n");        /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   xp=vector(1,npar);        
   dnewm=matrix(1,nlstate,1,npar);  #ifdef DEBUG
   doldm=matrix(1,nlstate,1,nlstate);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
          fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   hstepm=1*YEARM; /* Every year of age */  #endif
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   agelim = AGESUP;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          k=kmax;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        }
     if (stepm >= YEARM) hstepm=1;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          k=kmax; l=lmax*10.;
     gradg=matrix(1,npar,1,nlstate);        }
     gp=vector(1,nlstate);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     gm=vector(1,nlstate);          delts=delt;
         }
     for(theta=1; theta <=npar; theta++){      }
       for(i=1; i<=npar; i++){ /* Computes gradient */    }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    delti[theta]=delts;
       }    return res; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    
       for(i=1;i<=nlstate;i++)  }
         gp[i] = prlim[i][i];  
      double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
       for(i=1; i<=npar; i++) /* Computes gradient */  {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    int i;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int l=1, l1, lmax=20;
       for(i=1;i<=nlstate;i++)    double k1,k2,k3,k4,res,fx;
         gm[i] = prlim[i][i];    double p2[NPARMAX+1];
     int k;
       for(i=1;i<=nlstate;i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    fx=func(x);
     } /* End theta */    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
     trgradg =matrix(1,nlstate,1,npar);      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     for(j=1; j<=nlstate;j++)      k1=func(p2)-fx;
       for(theta=1; theta <=npar; theta++)    
         trgradg[j][theta]=gradg[theta][j];      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     for(i=1;i<=nlstate;i++)      k2=func(p2)-fx;
       varpl[i][(int)age] =0.;    
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      p2[thetai]=x[thetai]-delti[thetai]/k;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     for(i=1;i<=nlstate;i++)      k3=func(p2)-fx;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    
       p2[thetai]=x[thetai]-delti[thetai]/k;
     fprintf(ficresvpl,"%.0f ",age );      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     for(i=1; i<=nlstate;i++)      k4=func(p2)-fx;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     fprintf(ficresvpl,"\n");  #ifdef DEBUG
     free_vector(gp,1,nlstate);      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     free_vector(gm,1,nlstate);      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     free_matrix(gradg,1,npar,1,nlstate);  #endif
     free_matrix(trgradg,1,nlstate,1,npar);    }
   } /* End age */    return res;
   }
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);  /************** Inverse of matrix **************/
   free_matrix(dnewm,1,nlstate,1,nlstate);  void ludcmp(double **a, int n, int *indx, double *d) 
   { 
 }    int i,imax,j,k; 
     double big,dum,sum,temp; 
 /************ Variance of one-step probabilities  ******************/    double *vv; 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)   
 {    vv=vector(1,n); 
   int i, j, i1, k1, j1, z1;    *d=1.0; 
   int k=0,l, cptcode;    for (i=1;i<=n;i++) { 
   double **dnewm,**doldm;      big=0.0; 
   double *xp;      for (j=1;j<=n;j++) 
   double *gp, *gm;        if ((temp=fabs(a[i][j])) > big) big=temp; 
   double **gradg, **trgradg;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   double age,agelim, cov[NCOVMAX];      vv[i]=1.0/big; 
   int theta;    } 
   char fileresprob[FILENAMELENGTH];    for (j=1;j<=n;j++) { 
   char fileresprobcov[FILENAMELENGTH];      for (i=1;i<j;i++) { 
   char fileresprobcor[FILENAMELENGTH];        sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   strcpy(fileresprob,"prob");        a[i][j]=sum; 
   strcat(fileresprob,fileres);      } 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      big=0.0; 
     printf("Problem with resultfile: %s\n", fileresprob);      for (i=j;i<=n;i++) { 
   }        sum=a[i][j]; 
   strcpy(fileresprobcov,"probcov");        for (k=1;k<j;k++) 
   strcat(fileresprobcov,fileres);          sum -= a[i][k]*a[k][j]; 
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {        a[i][j]=sum; 
     printf("Problem with resultfile: %s\n", fileresprobcov);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   }          big=dum; 
   strcpy(fileresprobcor,"probcor");          imax=i; 
   strcat(fileresprobcor,fileres);        } 
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {      } 
     printf("Problem with resultfile: %s\n", fileresprobcor);      if (j != imax) { 
   }        for (k=1;k<=n;k++) { 
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);          dum=a[imax][k]; 
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);          a[imax][k]=a[j][k]; 
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);          a[j][k]=dum; 
          } 
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");        *d = -(*d); 
   fprintf(ficresprob,"# Age");        vv[imax]=vv[j]; 
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");      } 
   fprintf(ficresprobcov,"# Age");      indx[j]=imax; 
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");      if (a[j][j] == 0.0) a[j][j]=TINY; 
   fprintf(ficresprobcov,"# Age");      if (j != n) { 
   for(i=1; i<=nlstate;i++)        dum=1.0/(a[j][j]); 
     for(j=1; j<=(nlstate+ndeath);j++){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);      } 
       fprintf(ficresprobcov," p%1d-%1d ",i,j);    } 
       fprintf(ficresprobcor," p%1d-%1d ",i,j);    free_vector(vv,1,n);  /* Doesn't work */
     }    ;
   fprintf(ficresprob,"\n");  } 
   fprintf(ficresprobcov,"\n");  
   fprintf(ficresprobcor,"\n");  void lubksb(double **a, int n, int *indx, double b[]) 
   xp=vector(1,npar);  { 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    int i,ii=0,ip,j; 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    double sum; 
     
   cov[1]=1;    for (i=1;i<=n;i++) { 
   j=cptcoveff;      ip=indx[i]; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      sum=b[ip]; 
   j1=0;      b[ip]=b[i]; 
   for(k1=1; k1<=1;k1++){      if (ii) 
     for(i1=1; i1<=ncodemax[k1];i1++){        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     j1++;      else if (sum) ii=i; 
       b[i]=sum; 
     if  (cptcovn>0) {    } 
       fprintf(ficresprob, "\n#********** Variable ");    for (i=n;i>=1;i--) { 
       fprintf(ficresprobcov, "\n#********** Variable ");      sum=b[i]; 
       fprintf(ficresprobcor, "\n#********** Variable ");      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      b[i]=sum/a[i][i]; 
       fprintf(ficresprob, "**********\n#");    } 
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  } 
       fprintf(ficresprobcov, "**********\n#");  
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  void pstamp(FILE *fichier)
       fprintf(ficresprobcor, "**********\n#");  {
     }    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
      }
       for (age=bage; age<=fage; age ++){  
         cov[2]=age;  /************ Frequencies ********************/
         for (k=1; k<=cptcovn;k++) {  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[])
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];  {  /* Some frequencies */
         }    
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
         for (k=1; k<=cptcovprod;k++)    int first;
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    double ***freq; /* Frequencies */
            double *pp, **prop;
         gradg=matrix(1,npar,1,9);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
         trgradg=matrix(1,9,1,npar);    char fileresp[FILENAMELENGTH];
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    pp=vector(1,nlstate);
        prop=matrix(1,nlstate,iagemin,iagemax+3);
         for(theta=1; theta <=npar; theta++){    strcpy(fileresp,"p");
           for(i=1; i<=npar; i++)    strcat(fileresp,fileres);
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    if((ficresp=fopen(fileresp,"w"))==NULL) {
                printf("Problem with prevalence resultfile: %s\n", fileresp);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
                exit(0);
           k=0;    }
           for(i=1; i<= (nlstate+ndeath); i++){    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
             for(j=1; j<=(nlstate+ndeath);j++){    j1=0;
               k=k+1;    
               gp[k]=pmmij[i][j];    j=cptcoveff;
             }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           }  
              first=1;
           for(i=1; i<=npar; i++)  
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    for(k1=1; k1<=j;k1++){
          for(i1=1; i1<=ncodemax[k1];i1++){
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        j1++;
           k=0;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           for(i=1; i<=(nlstate+ndeath); i++){          scanf("%d", i);*/
             for(j=1; j<=(nlstate+ndeath);j++){        for (i=-5; i<=nlstate+ndeath; i++)  
               k=k+1;          for (jk=-5; jk<=nlstate+ndeath; jk++)  
               gm[k]=pmmij[i][j];            for(m=iagemin; m <= iagemax+3; m++)
             }              freq[i][jk][m]=0;
           }  
            for (i=1; i<=nlstate; i++)  
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        for(m=iagemin; m <= iagemax+3; m++)
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            prop[i][m]=0;
         }        
         dateintsum=0;
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)        k2cpt=0;
           for(theta=1; theta <=npar; theta++)        for (i=1; i<=imx; i++) {
             trgradg[j][theta]=gradg[theta][j];          bool=1;
                  if  (cptcovn>0) {
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);            for (z1=1; z1<=cptcoveff; z1++) 
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                        bool=0;
         pmij(pmmij,cov,ncovmodel,x,nlstate);          }
                  if (bool==1){
         k=0;            for(m=firstpass; m<=lastpass; m++){
         for(i=1; i<=(nlstate+ndeath); i++){              k2=anint[m][i]+(mint[m][i]/12.);
           for(j=1; j<=(nlstate+ndeath);j++){              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
             k=k+1;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
             gm[k]=pmmij[i][j];                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           }                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
         }                if (m<lastpass) {
                        freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
         /*printf("\n%d ",(int)age);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){                }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));                
      }*/                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
         fprintf(ficresprob,"\n%d ",(int)age);                  k2cpt++;
         fprintf(ficresprobcov,"\n%d ",(int)age);                }
         fprintf(ficresprobcor,"\n%d ",(int)age);                /*}*/
             }
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)          }
           fprintf(ficresprob,"%12.3e (%12.3e) ",gm[i],sqrt(doldm[i][j]));        }
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){         
           fprintf(ficresprobcov,"%12.3e ",gm[i]);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
           fprintf(ficresprobcor,"%12.3e ",gm[i]);        pstamp(ficresp);
         }        if  (cptcovn>0) {
         i=0;          fprintf(ficresp, "\n#********** Variable "); 
         for (k=1; k<=(nlstate);k++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           for (l=1; l<=(nlstate+ndeath);l++){          fprintf(ficresp, "**********\n#");
             i=i++;        }
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);        for(i=1; i<=nlstate;i++) 
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
             for (j=1; j<=i;j++){        fprintf(ficresp, "\n");
               fprintf(ficresprobcov," %12.3e",doldm[i][j]);        
               fprintf(ficresprobcor," %12.3e",doldm[i][j]/sqrt(doldm[i][i])/sqrt(doldm[j][j]));        for(i=iagemin; i <= iagemax+3; i++){
             }          if(i==iagemax+3){
           }            fprintf(ficlog,"Total");
         }          }else{
       }            if(first==1){
     }              first=0;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));              printf("See log file for details...\n");
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));            }
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            fprintf(ficlog,"Age %d", i);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          }
   }          for(jk=1; jk <=nlstate ; jk++){
   free_vector(xp,1,npar);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   fclose(ficresprob);              pp[jk] += freq[jk][m][i]; 
   fclose(ficresprobcov);          }
   fclose(ficresprobcor);          for(jk=1; jk <=nlstate ; jk++){
 }            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
 /******************* Printing html file ***********/              if(first==1){
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                   int lastpass, int stepm, int weightopt, char model[],\              }
                   int imx,int jmin, int jmax, double jmeanint,char optionfile[], \              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                   char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\            }else{
                   char version[], int popforecast, int estepm ,\              if(first==1)
                   double jprev1, double mprev1,double anprev1, \                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                   double jprev2, double mprev2,double anprev2){              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   int jj1, k1, i1, cpt;            }
   FILE *fichtm;          }
   /*char optionfilehtm[FILENAMELENGTH];*/  
           for(jk=1; jk <=nlstate ; jk++){
   strcpy(optionfilehtm,optionfile);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   strcat(optionfilehtm,".htm");              pp[jk] += freq[jk][m][i];
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          }       
     printf("Problem with %s \n",optionfilehtm), exit(0);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   }            pos += pp[jk];
             posprop += prop[jk][i];
   fprintf(fichtm,"<body> <font size=\"2\">%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          for(jk=1; jk <=nlstate ; jk++){
 \n            if(pos>=1.e-5){
 Total number of observations=%d <br>\n              if(first==1)
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 <hr  size=\"2\" color=\"#EC5E5E\">              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
  <ul><li>Parameter files<br>\n            }else{
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n              if(first==1)
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n            }
  - 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            if( i <= iagemax){
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n              if(pos>=1.e-5){
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
  - Life expectancies by age and initial health status (estepm=%2d months):                /*probs[i][jk][j1]= pp[jk]/pos;*/
    <a href=\"e%s\">e%s</a> <br>\n</li>", \                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);              }
               else
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n            }
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n          }
  - 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          for(jk=-1; jk <=nlstate+ndeath; jk++)
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n            for(m=-1; m <=nlstate+ndeath; m++)
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n              if(freq[jk][m][i] !=0 ) {
  - 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(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
  if(popforecast==1) fprintf(fichtm,"\n                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n              }
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n          if(i <= iagemax)
         <br>",fileres,fileres,fileres,fileres);            fprintf(ficresp,"\n");
  else          if(first==1)
    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);            printf("Others in log...\n");
 fprintf(fichtm," <li>Graphs</li><p>");          fprintf(ficlog,"\n");
         }
  m=cptcoveff;      }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    }
     dateintmean=dateintsum/k2cpt; 
  jj1=0;   
  for(k1=1; k1<=m;k1++){    fclose(ficresp);
    for(i1=1; i1<=ncodemax[k1];i1++){    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
      jj1++;    free_vector(pp,1,nlstate);
      if (cptcovn > 0) {    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    /* End of Freq */
        for (cpt=1; cpt<=cptcoveff;cpt++)  }
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);  
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");  /************ Prevalence ********************/
      }  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)
      /* Pij */  {  
      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>    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);           in each health status at the date of interview (if between dateprev1 and dateprev2).
      /* Quasi-incidences */       We still use firstpass and lastpass as another selection.
      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);   
        /* Stable prevalence in each health state */    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
        for(cpt=1; cpt<nlstate;cpt++){    double ***freq; /* Frequencies */
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    double *pp, **prop;
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    double pos,posprop; 
        }    double  y2; /* in fractional years */
     for(cpt=1; cpt<=nlstate;cpt++) {    int iagemin, iagemax;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  
 interval) in state (%d): v%s%d%d.png <br>    iagemin= (int) agemin;
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      iagemax= (int) agemax;
      }    /*pp=vector(1,nlstate);*/
      for(cpt=1; cpt<=nlstate;cpt++) {    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    j1=0;
      }    
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    j=cptcoveff;
 health expectancies in states (1) and (2): e%s%d.png<br>    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    
 fprintf(fichtm,"\n</body>");    for(k1=1; k1<=j;k1++){
    }      for(i1=1; i1<=ncodemax[k1];i1++){
  }        j1++;
 fclose(fichtm);        
 }        for (i=1; i<=nlstate; i++)  
           for(m=iagemin; m <= iagemax+3; m++)
 /******************* Gnuplot file **************/            prop[i][m]=0.0;
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){       
         for (i=1; i<=imx; i++) { /* Each individual */
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          bool=1;
   int ng;          if  (cptcovn>0) {
   strcpy(optionfilegnuplot,optionfilefiname);            for (z1=1; z1<=cptcoveff; z1++) 
   strcat(optionfilegnuplot,".gp");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {                bool=0;
     printf("Problem with file %s",optionfilegnuplot);          } 
   }          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
 #ifdef windows              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     fprintf(ficgp,"cd \"%s\" \n",pathc);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
 #endif                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 m=pow(2,cptcoveff);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                  if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
  /* 1eme*/                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   for (cpt=1; cpt<= nlstate ; cpt ++) {                  /*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]]);*/
    for (k1=1; k1<= m ; k1 ++) {                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
 #ifdef windows                } 
      fprintf(ficgp,"\nset out \"v%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] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);            } /* end selection of waves */
 #endif          }
 #ifdef unix        }
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        for(i=iagemin; i <= iagemax+3; i++){  
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);          
 #endif          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
 for (i=1; i<= nlstate ; i ++) {          } 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(jk=1; jk <=nlstate ; jk++){     
 }            if( i <=  iagemax){ 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);              if(posprop>=1.e-5){ 
     for (i=1; i<= nlstate ; i ++) {                probs[i][jk][j1]= prop[jk][i]/posprop;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");            } 
 }          }/* end jk */ 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        }/* end i */ 
      for (i=1; i<= nlstate ; i ++) {      } /* end i1 */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    } /* end k1 */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    
 }      /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    /*free_vector(pp,1,nlstate);*/
 #ifdef unix    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");  }  /* End of prevalence */
 #endif  
    }  /************* Waves Concatenation ***************/
   }  
   /*2 eme*/  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)
   {
   for (k1=1; k1<= m ; k1 ++) {    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);       Death is a valid wave (if date is known).
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
           dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     for (i=1; i<= nlstate+1 ; i ++) {       and mw[mi+1][i]. dh depends on stepm.
       k=2*i;       */
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {    int i, mi, m;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   else fprintf(ficgp," \%%*lf (\%%*lf)");       double sum=0., jmean=0.;*/
 }      int first;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    int j, k=0,jk, ju, jl;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    double sum=0.;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    first=0;
       for (j=1; j<= nlstate+1 ; j ++) {    jmin=1e+5;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    jmax=-1;
         else fprintf(ficgp," \%%*lf (\%%*lf)");    jmean=0.;
 }      for(i=1; i<=imx; i++){
       fprintf(ficgp,"\" t\"\" w l 0,");      mi=0;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      m=firstpass;
       for (j=1; j<= nlstate+1 ; j ++) {      while(s[m][i] <= nlstate){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   else fprintf(ficgp," \%%*lf (\%%*lf)");          mw[++mi][i]=m;
 }          if(m >=lastpass)
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          break;
       else fprintf(ficgp,"\" t\"\" w l 0,");        else
     }          m++;
   }      }/* end while */
        if (s[m][i] > nlstate){
   /*3eme*/        mi++;     /* Death is another wave */
         /* if(mi==0)  never been interviewed correctly before death */
   for (k1=1; k1<= m ; k1 ++) {           /* Only death is a correct wave */
     for (cpt=1; cpt<= nlstate ; cpt ++) {        mw[mi][i]=m;
       k=2+nlstate*(2*cpt-2);      }
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);      wav[i]=mi;
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      if(mi==0){
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        nbwarn++;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        if(first==0){
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          first=1;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        }
         if(first==1){
 */          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
       for (i=1; i< nlstate ; i ++) {        }
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);      } /* end mi==0 */
     } /* End individuals */
       }  
     }    for(i=1; i<=imx; i++){
   }      for(mi=1; mi<wav[i];mi++){
          if (stepm <=0)
   /* CV preval stat */          dh[mi][i]=1;
     for (k1=1; k1<= m ; k1 ++) {        else{
     for (cpt=1; cpt<nlstate ; cpt ++) {          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       k=3;            if (agedc[i] < 2*AGESUP) {
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);              if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
       for (i=1; i< nlstate ; i ++)                nberr++;
         fprintf(ficgp,"+$%d",k+i+1);                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]);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);                j=1; /* Temporary Dangerous patch */
                      printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
       l=3+(nlstate+ndeath)*cpt;                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]);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
       for (i=1; i< nlstate ; i ++) {              }
         l=3+(nlstate+ndeath)*cpt;              k=k+1;
         fprintf(ficgp,"+$%d",l+i+1);              if (j >= jmax){
       }                jmax=j;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                  ijmax=i;
     }              }
   }                if (j <= jmin){
                  jmin=j;
   /* proba elementaires */                ijmin=i;
    for(i=1,jk=1; i <=nlstate; i++){              }
     for(k=1; k <=(nlstate+ndeath); k++){              sum=sum+j;
       if (k != i) {              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         for(j=1; j <=ncovmodel; j++){              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                    }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          }
           jk++;          else{
           fprintf(ficgp,"\n");            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         }  /*        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]); */
       }  
     }            k=k+1;
    }            if (j >= jmax) {
               jmax=j;
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/              ijmax=i;
      for(jk=1; jk <=m; jk++) {            }
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);            else if (j <= jmin){
        if (ng==2)              jmin=j;
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");              ijmin=i;
        else            }
          fprintf(ficgp,"\nset title \"Probability\"\n");            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);            /*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]);*/
        i=1;            if(j<0){
        for(k2=1; k2<=nlstate; k2++) {              nberr++;
          k3=i;              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
          for(k=1; k<=(nlstate+ndeath); k++) {              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
            if (k != k2){            }
              if(ng==2)            sum=sum+j;
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);          }
              else          jk= j/stepm;
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          jl= j -jk*stepm;
              ij=1;          ju= j -(jk+1)*stepm;
              for(j=3; j <=ncovmodel; j++) {          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {            if(jl==0){
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);              dh[mi][i]=jk;
                  ij++;              bh[mi][i]=0;
                }            }else{ /* We want a negative bias in order to only have interpolation ie
                else                    * at the price of an extra matrix product in likelihood */
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              dh[mi][i]=jk+1;
              }              bh[mi][i]=ju;
              fprintf(ficgp,")/(1");            }
                        }else{
              for(k1=1; k1 <=nlstate; k1++){              if(jl <= -ju){
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);              dh[mi][i]=jk;
                ij=1;              bh[mi][i]=jl;       /* bias is positive if real duration
                for(j=3; j <=ncovmodel; j++){                                   * is higher than the multiple of stepm and negative otherwise.
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                                   */
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            }
                    ij++;            else{
                  }              dh[mi][i]=jk+1;
                  else              bh[mi][i]=ju;
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            }
                }            if(dh[mi][i]==0){
                fprintf(ficgp,")");              dh[mi][i]=1; /* At least one step */
              }              bh[mi][i]=ju; /* At least one step */
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");            }
              i=i+ncovmodel;          } /* end if mle */
            }        }
          }      } /* end wave */
        }    }
      }    jmean=sum/k;
    }    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);
    fclose(ficgp);    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);
 }  /* end gnuplot */   }
   
   /*********** Tricode ****************************/
 /*************** Moving average **************/  void tricode(int *Tvar, int **nbcode, int imx)
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){  {
     
   int i, cpt, cptcod;    int Ndum[20],ij=1, k, j, i, maxncov=19;
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    int cptcode=0;
       for (i=1; i<=nlstate;i++)    cptcoveff=0; 
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)   
           mobaverage[(int)agedeb][i][cptcod]=0.;    for (k=0; k<maxncov; k++) Ndum[k]=0;
        for (k=1; k<=7; k++) ncodemax[k]=0;
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){  
       for (i=1; i<=nlstate;i++){    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
           for (cpt=0;cpt<=4;cpt++){                                 modality*/ 
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
           }        Ndum[ij]++; /*store the modality */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         }        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
       }                                         Tvar[j]. If V=sex and male is 0 and 
     }                                         female is 1, then  cptcode=1.*/
          }
 }  
       for (i=0; i<=cptcode; i++) {
         if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
 /************** Forecasting ******************/      }
 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){  
        ij=1; 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      for (i=1; i<=ncodemax[j]; i++) {
   int *popage;        for (k=0; k<= maxncov; k++) {
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          if (Ndum[k] != 0) {
   double *popeffectif,*popcount;            nbcode[Tvar[j]][ij]=k; 
   double ***p3mat;            /* 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; */
   char fileresf[FILENAMELENGTH];            
             ij++;
  agelim=AGESUP;          }
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          if (ij > ncodemax[j]) break; 
         }  
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      } 
      }  
    
   strcpy(fileresf,"f");   for (k=0; k< maxncov; k++) Ndum[k]=0;
   strcat(fileresf,fileres);  
   if((ficresf=fopen(fileresf,"w"))==NULL) {   for (i=1; i<=ncovmodel-2; i++) { 
     printf("Problem with forecast resultfile: %s\n", fileresf);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   }     ij=Tvar[i];
   printf("Computing forecasting: result on file '%s' \n", fileresf);     Ndum[ij]++;
    }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
    ij=1;
   if (mobilav==1) {   for (i=1; i<= maxncov; i++) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     if((Ndum[i]!=0) && (i<=ncovcol)){
     movingaverage(agedeb, fage, ageminpar, mobaverage);       Tvaraff[ij]=i; /*For printing */
   }       ij++;
      }
   stepsize=(int) (stepm+YEARM-1)/YEARM;   }
   if (stepm<=12) stepsize=1;   
     cptcoveff=ij-1; /*Number of simple covariates*/
   agelim=AGESUP;  }
    
   hstepm=1;  /*********** Health Expectancies ****************/
   hstepm=hstepm/stepm;  
   yp1=modf(dateintmean,&yp);  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[] )
   anprojmean=yp;  
   yp2=modf((yp1*12),&yp);  {
   mprojmean=yp;    /* Health expectancies, no variances */
   yp1=modf((yp2*30.5),&yp);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   jprojmean=yp;    double age, agelim, hf;
   if(jprojmean==0) jprojmean=1;    double ***p3mat;
   if(mprojmean==0) jprojmean=1;    double eip;
    
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    pstamp(ficreseij);
      fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   for(cptcov=1;cptcov<=i2;cptcov++){    fprintf(ficreseij,"# Age");
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    for(i=1; i<=nlstate;i++){
       k=k+1;      for(j=1; j<=nlstate;j++){
       fprintf(ficresf,"\n#******");        fprintf(ficreseij," e%1d%1d ",i,j);
       for(j=1;j<=cptcoveff;j++) {      }
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficreseij," e%1d. ",i);
       }    }
       fprintf(ficresf,"******\n");    fprintf(ficreseij,"\n");
       fprintf(ficresf,"# StartingAge FinalAge");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    
          if(estepm < stepm){
            printf ("Problem %d lower than %d\n",estepm, stepm);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    }
         fprintf(ficresf,"\n");    else  hstepm=estepm;   
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){     * if stepm=24 months pijx are given only every 2 years and by summing them
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);     * we are calculating an estimate of the Life Expectancy assuming a linear 
           nhstepm = nhstepm/hstepm;     * progression in between and thus overestimating or underestimating according
               * to the curvature of the survival function. If, for the same date, we 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           oldm=oldms;savm=savms;     * to compare the new estimate of Life expectancy with the same linear 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       * hypothesis. A more precise result, taking into account a more precise
             * curvature will be obtained if estepm is as small as stepm. */
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {    /* For example we decided to compute the life expectancy with the smallest unit */
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    /* 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 
             for(j=1; j<=nlstate+ndeath;j++) {       nstepm is the number of stepm from age to agelin. 
               kk1=0.;kk2=0;       Look at hpijx to understand the reason of that which relies in memory size
               for(i=1; i<=nlstate;i++) {                     and note for a fixed period like estepm months */
                 if (mobilav==1)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];       survival function given by stepm (the optimization length). Unfortunately it
                 else {       means that if the survival funtion is printed only each two years of age and if
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];       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.
                    */
               }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
               if (h==(int)(calagedate+12*cpt)){  
                 fprintf(ficresf," %.3f", kk1);    agelim=AGESUP;
                            /* nhstepm age range expressed in number of stepm */
               }    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
             }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           }    /* if (stepm >= YEARM) hstepm=1;*/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         }    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }  
     }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
                 in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   fclose(ficresf);      
 }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 /************** Forecasting ******************/      
 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){      printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      
   int *popage;      /* Computing expectancies */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      for(i=1; i<=nlstate;i++)
   double *popeffectif,*popcount;        for(j=1; j<=nlstate;j++)
   double ***p3mat,***tabpop,***tabpopprev;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   char filerespop[FILENAMELENGTH];            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            /* 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]);*/
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   agelim=AGESUP;          }
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;  
        fprintf(ficreseij,"%3.0f",age );
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      for(i=1; i<=nlstate;i++){
          eip=0;
          for(j=1; j<=nlstate;j++){
   strcpy(filerespop,"pop");          eip +=eij[i][j][(int)age];
   strcat(filerespop,fileres);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        }
     printf("Problem with forecast resultfile: %s\n", filerespop);        fprintf(ficreseij,"%9.4f", eip );
   }      }
   printf("Computing forecasting: result on file '%s' \n", filerespop);      fprintf(ficreseij,"\n");
       
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (mobilav==1) {    printf("\n");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficlog,"\n");
     movingaverage(agedeb, fage, ageminpar, mobaverage);    
   }  }
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;  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[] )
   if (stepm<=12) stepsize=1;  
    {
   agelim=AGESUP;    /* Covariances of health expectancies eij and of total life expectancies according
       to initial status i, ei. .
   hstepm=1;    */
   hstepm=hstepm/stepm;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
      double age, agelim, hf;
   if (popforecast==1) {    double ***p3matp, ***p3matm, ***varhe;
     if((ficpop=fopen(popfile,"r"))==NULL) {    double **dnewm,**doldm;
       printf("Problem with population file : %s\n",popfile);exit(0);    double *xp, *xm;
     }    double **gp, **gm;
     popage=ivector(0,AGESUP);    double ***gradg, ***trgradg;
     popeffectif=vector(0,AGESUP);    int theta;
     popcount=vector(0,AGESUP);  
        double eip, vip;
     i=1;    
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
        xp=vector(1,npar);
     imx=i;    xm=vector(1,npar);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    dnewm=matrix(1,nlstate*nlstate,1,npar);
   }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
   for(cptcov=1;cptcov<=i2;cptcov++){    pstamp(ficresstdeij);
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
       k=k+1;    fprintf(ficresstdeij,"# Age");
       fprintf(ficrespop,"\n#******");    for(i=1; i<=nlstate;i++){
       for(j=1;j<=cptcoveff;j++) {      for(j=1; j<=nlstate;j++)
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       }      fprintf(ficresstdeij," e%1d. ",i);
       fprintf(ficrespop,"******\n");    }
       fprintf(ficrespop,"# Age");    fprintf(ficresstdeij,"\n");
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  
       if (popforecast==1)  fprintf(ficrespop," [Population]");    pstamp(ficrescveij);
          fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
       for (cpt=0; cpt<=0;cpt++) {    fprintf(ficrescveij,"# Age");
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      for(i=1; i<=nlstate;i++)
              for(j=1; j<=nlstate;j++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        cptj= (j-1)*nlstate+i;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        for(i2=1; i2<=nlstate;i2++)
           nhstepm = nhstepm/hstepm;          for(j2=1; j2<=nlstate;j2++){
                      cptj2= (j2-1)*nlstate+i2;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            if(cptj2 <= cptj)
           oldm=oldms;savm=savms;              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            }
              }
           for (h=0; h<=nhstepm; h++){    fprintf(ficrescveij,"\n");
             if (h==(int) (calagedate+YEARM*cpt)) {    
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    if(estepm < stepm){
             }      printf ("Problem %d lower than %d\n",estepm, stepm);
             for(j=1; j<=nlstate+ndeath;j++) {    }
               kk1=0.;kk2=0;    else  hstepm=estepm;   
               for(i=1; i<=nlstate;i++) {                  /* We compute the life expectancy from trapezoids spaced every estepm months
                 if (mobilav==1)     * This is mainly to measure the difference between two models: for example
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];     * if stepm=24 months pijx are given only every 2 years and by summing them
                 else {     * we are calculating an estimate of the Life Expectancy assuming a linear 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];     * progression in between and thus overestimating or underestimating according
                 }     * to the curvature of the survival function. If, for the same date, we 
               }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
               if (h==(int)(calagedate+12*cpt)){     * to compare the new estimate of Life expectancy with the same linear 
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;     * hypothesis. A more precise result, taking into account a more precise
                   /*fprintf(ficrespop," %.3f", kk1);     * curvature will be obtained if estepm is as small as stepm. */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  
               }    /* For example we decided to compute the life expectancy with the smallest unit */
             }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
             for(i=1; i<=nlstate;i++){       nhstepm is the number of hstepm from age to agelim 
               kk1=0.;       nstepm is the number of stepm from age to agelin. 
                 for(j=1; j<=nlstate;j++){       Look at hpijx to understand the reason of that which relies in memory size
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];       and note for a fixed period like estepm months */
                 }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];       survival function given by stepm (the optimization length). Unfortunately it
             }       means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)       results. So we changed our mind and took the option of the best precision.
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    */
           }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }    /* If stepm=6 months */
       }    /* nhstepm age range expressed in number of stepm */
      agelim=AGESUP;
   /******/    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    /* if (stepm >= YEARM) hstepm=1;*/
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           nhstepm = nhstepm/hstepm;    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
           oldm=oldms;savm=savms;    gp=matrix(0,nhstepm,1,nlstate*nlstate);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {    for (age=bage; age<=fage; age ++){ 
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
             for(j=1; j<=nlstate+ndeath;j++) {         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
               kk1=0.;kk2=0;   
               for(i=1; i<=nlstate;i++) {                    hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      
               }      /* Computing  Variances of health expectancies */
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
             }         decrease memory allocation */
           }      for(theta=1; theta <=npar; theta++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(i=1; i<=npar; i++){ 
         }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }          xm[i] = x[i] - (i==theta ?delti[theta]:0);
    }        }
   }        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
          hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    
         for(j=1; j<= nlstate; j++){
   if (popforecast==1) {          for(i=1; i<=nlstate; i++){
     free_ivector(popage,0,AGESUP);            for(h=0; h<=nhstepm-1; h++){
     free_vector(popeffectif,0,AGESUP);              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
     free_vector(popcount,0,AGESUP);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
   }            }
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }
   fclose(ficrespop);       
 }        for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
 /***********************************************/            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
 /**************** Main Program *****************/          }
 /***********************************************/      }/* End theta */
       
 int main(int argc, char *argv[])      
 {      for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;          for(theta=1; theta <=npar; theta++)
   double agedeb, agefin,hf;            trgradg[h][j][theta]=gradg[h][theta][j];
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      
   
   double fret;       for(ij=1;ij<=nlstate*nlstate;ij++)
   double **xi,tmp,delta;        for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
   double dum; /* Dummy variable */  
   double ***p3mat;       printf("%d|",(int)age);fflush(stdout);
   int *indx;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   char line[MAXLINE], linepar[MAXLINE];       for(h=0;h<=nhstepm-1;h++){
   char title[MAXLINE];        for(k=0;k<=nhstepm-1;k++){
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
            for(ij=1;ij<=nlstate*nlstate;ij++)
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];            for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
   char filerest[FILENAMELENGTH];        }
   char fileregp[FILENAMELENGTH];      }
   char popfile[FILENAMELENGTH];      /* Computing expectancies */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   int firstobs=1, lastobs=10;      for(i=1; i<=nlstate;i++)
   int sdeb, sfin; /* Status at beginning and end */        for(j=1; j<=nlstate;j++)
   int c,  h , cpt,l;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   int ju,jl, mi;            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   int mobilav=0,popforecast=0;  
   int hstepm, nhstepm;          }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;  
       fprintf(ficresstdeij,"%3.0f",age );
   double bage, fage, age, agelim, agebase;      for(i=1; i<=nlstate;i++){
   double ftolpl=FTOL;        eip=0.;
   double **prlim;        vip=0.;
   double *severity;        for(j=1; j<=nlstate;j++){
   double ***param; /* Matrix of parameters */          eip += eij[i][j][(int)age];
   double  *p;          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
   double **matcov; /* Matrix of covariance */            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
   double ***delti3; /* Scale */          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
   double *delti; /* Scale */        }
   double ***eij, ***vareij;        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
   double **varpl; /* Variances of prevalence limits by age */      }
   double *epj, vepp;      fprintf(ficresstdeij,"\n");
   double kk1, kk2;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;      fprintf(ficrescveij,"%3.0f",age );
        for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   char version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";          cptj= (j-1)*nlstate+i;
   char *alph[]={"a","a","b","c","d","e"}, str[4];          for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
   char z[1]="c", occ;              if(cptj2 <= cptj)
 #include <sys/time.h>                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
 #include <time.h>            }
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        }
        fprintf(ficrescveij,"\n");
   /* long total_usecs;     
   struct timeval start_time, end_time;    }
      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   getcwd(pathcd, size);    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   printf("\n%s",version);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if(argc <=1){    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\nEnter the parameter file name: ");    printf("\n");
     scanf("%s",pathtot);    fprintf(ficlog,"\n");
   }  
   else{    free_vector(xm,1,npar);
     strcpy(pathtot,argv[1]);    free_vector(xp,1,npar);
   }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   /*cygwin_split_path(pathtot,path,optionfile);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  }
   /* cutv(path,optionfile,pathtot,'\\');*/  
   /************ Variance ******************/
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  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[])
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  {
   chdir(path);    /* Variance of health expectancies */
   replace(pathc,path);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
 /*-------- arguments in the command line --------*/    double **dnewm,**doldm;
     double **dnewmp,**doldmp;
   strcpy(fileres,"r");    int i, j, nhstepm, hstepm, h, nstepm ;
   strcat(fileres, optionfilefiname);    int k, cptcode;
   strcat(fileres,".txt");    /* Other files have txt extension */    double *xp;
     double **gp, **gm;  /* for var eij */
   /*---------arguments file --------*/    double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    double *gpp, *gmp; /* for var p point j */
     printf("Problem with optionfile %s\n",optionfile);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     goto end;    double ***p3mat;
   }    double age,agelim, hf;
     double ***mobaverage;
   strcpy(filereso,"o");    int theta;
   strcat(filereso,fileres);    char digit[4];
   if((ficparo=fopen(filereso,"w"))==NULL) {    char digitp[25];
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  
   }    char fileresprobmorprev[FILENAMELENGTH];
   
   /* Reads comments: lines beginning with '#' */    if(popbased==1){
   while((c=getc(ficpar))=='#' && c!= EOF){      if(mobilav!=0)
     ungetc(c,ficpar);        strcpy(digitp,"-populbased-mobilav-");
     fgets(line, MAXLINE, ficpar);      else strcpy(digitp,"-populbased-nomobil-");
     puts(line);    }
     fputs(line,ficparo);    else 
   }      strcpy(digitp,"-stablbased-");
   ungetc(c,ficpar);  
     if (mobilav!=0) {
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   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);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   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," Error in movingaverage mobilav=%d\n",mobilav);
 while((c=getc(ficpar))=='#' && c!= EOF){        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     ungetc(c,ficpar);      }
     fgets(line, MAXLINE, ficpar);    }
     puts(line);  
     fputs(line,ficparo);    strcpy(fileresprobmorprev,"prmorprev"); 
   }    sprintf(digit,"%-d",ij);
   ungetc(c,ficpar);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
      strcat(fileresprobmorprev,digit); /* Tvar to be done */
        strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   covar=matrix(0,NCOVMAX,1,n);    strcat(fileresprobmorprev,fileres);
   cptcovn=0;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   ncovmodel=2+cptcovn;    }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     
   /* Read guess parameters */    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   /* Reads comments: lines beginning with '#' */    pstamp(ficresprobmorprev);
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     ungetc(c,ficpar);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     fgets(line, MAXLINE, ficpar);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     puts(line);      fprintf(ficresprobmorprev," p.%-d SE",j);
     fputs(line,ficparo);      for(i=1; i<=nlstate;i++)
   }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   ungetc(c,ficpar);    }  
      fprintf(ficresprobmorprev,"\n");
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    fprintf(ficgp,"\n# Routine varevsij");
     for(i=1; i <=nlstate; i++)    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     for(j=1; j <=nlstate+ndeath-1; j++){    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");
       fscanf(ficpar,"%1d%1d",&i1,&j1);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
       fprintf(ficparo,"%1d%1d",i1,j1);  /*   } */
       printf("%1d%1d",i,j);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       for(k=1; k<=ncovmodel;k++){    pstamp(ficresvij);
         fscanf(ficpar," %lf",&param[i][j][k]);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
         printf(" %lf",param[i][j][k]);    if(popbased==1)
         fprintf(ficparo," %lf",param[i][j][k]);      fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
       }    else
       fscanf(ficpar,"\n");      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
       printf("\n");    fprintf(ficresvij,"# Age");
       fprintf(ficparo,"\n");    for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=nlstate;j++)
          fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    fprintf(ficresvij,"\n");
   
   p=param[1][1];    xp=vector(1,npar);
      dnewm=matrix(1,nlstate,1,npar);
   /* Reads comments: lines beginning with '#' */    doldm=matrix(1,nlstate,1,nlstate);
   while((c=getc(ficpar))=='#' && c!= EOF){    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     ungetc(c,ficpar);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     fgets(line, MAXLINE, ficpar);  
     puts(line);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     fputs(line,ficparo);    gpp=vector(nlstate+1,nlstate+ndeath);
   }    gmp=vector(nlstate+1,nlstate+ndeath);
   ungetc(c,ficpar);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    if(estepm < stepm){
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      printf ("Problem %d lower than %d\n",estepm, stepm);
   for(i=1; i <=nlstate; i++){    }
     for(j=1; j <=nlstate+ndeath-1; j++){    else  hstepm=estepm;   
       fscanf(ficpar,"%1d%1d",&i1,&j1);    /* For example we decided to compute the life expectancy with the smallest unit */
       printf("%1d%1d",i,j);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       fprintf(ficparo,"%1d%1d",i1,j1);       nhstepm is the number of hstepm from age to agelim 
       for(k=1; k<=ncovmodel;k++){       nstepm is the number of stepm from age to agelin. 
         fscanf(ficpar,"%le",&delti3[i][j][k]);       Look at hpijx to understand the reason of that which relies in memory size
         printf(" %le",delti3[i][j][k]);       and note for a fixed period like k years */
         fprintf(ficparo," %le",delti3[i][j][k]);    /* 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
       fscanf(ficpar,"\n");       means that if the survival funtion is printed every two years of age and if
       printf("\n");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       fprintf(ficparo,"\n");       results. So we changed our mind and took the option of the best precision.
     }    */
   }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   delti=delti3[1][1];    agelim = AGESUP;
      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   /* Reads comments: lines beginning with '#' */      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   while((c=getc(ficpar))=='#' && c!= EOF){      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     ungetc(c,ficpar);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fgets(line, MAXLINE, ficpar);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     puts(line);      gp=matrix(0,nhstepm,1,nlstate);
     fputs(line,ficparo);      gm=matrix(0,nhstepm,1,nlstate);
   }  
   ungetc(c,ficpar);  
        for(theta=1; theta <=npar; theta++){
   matcov=matrix(1,npar,1,npar);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   for(i=1; i <=npar; i++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     fscanf(ficpar,"%s",&str);        }
     printf("%s",str);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fprintf(ficparo,"%s",str);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     for(j=1; j <=i; j++){  
       fscanf(ficpar," %le",&matcov[i][j]);        if (popbased==1) {
       printf(" %.5le",matcov[i][j]);          if(mobilav ==0){
       fprintf(ficparo," %.5le",matcov[i][j]);            for(i=1; i<=nlstate;i++)
     }              prlim[i][i]=probs[(int)age][i][ij];
     fscanf(ficpar,"\n");          }else{ /* mobilav */ 
     printf("\n");            for(i=1; i<=nlstate;i++)
     fprintf(ficparo,"\n");              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
   for(i=1; i <=npar; i++)        }
     for(j=i+1;j<=npar;j++)    
       matcov[i][j]=matcov[j][i];        for(j=1; j<= nlstate; j++){
              for(h=0; h<=nhstepm; h++){
   printf("\n");            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
     /*-------- Rewriting paramater file ----------*/        }
      strcpy(rfileres,"r");    /* "Rparameterfile */        /* This for computing probability of death (h=1 means
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/           computed over hstepm matrices product = hstepm*stepm months) 
      strcat(rfileres,".");    /* */           as a weighted average of prlim.
      strcat(rfileres,optionfilext);    /* Other files have txt extension */        */
     if((ficres =fopen(rfileres,"w"))==NULL) {        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       printf("Problem writing new parameter file: %s\n", fileres);goto end;          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     fprintf(ficres,"#%s\n",version);        }    
            /* end probability of death */
     /*-------- data file ----------*/  
     if((fic=fopen(datafile,"r"))==NULL)    {        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
       printf("Problem with datafile: %s\n", datafile);goto end;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     n= lastobs;   
     severity = vector(1,maxwav);        if (popbased==1) {
     outcome=imatrix(1,maxwav+1,1,n);          if(mobilav ==0){
     num=ivector(1,n);            for(i=1; i<=nlstate;i++)
     moisnais=vector(1,n);              prlim[i][i]=probs[(int)age][i][ij];
     annais=vector(1,n);          }else{ /* mobilav */ 
     moisdc=vector(1,n);            for(i=1; i<=nlstate;i++)
     andc=vector(1,n);              prlim[i][i]=mobaverage[(int)age][i][ij];
     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 */        for(j=1; j<= nlstate; j++){
     mint=matrix(1,maxwav,1,n);          for(h=0; h<=nhstepm; h++){
     anint=matrix(1,maxwav,1,n);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     s=imatrix(1,maxwav+1,1,n);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     adl=imatrix(1,maxwav+1,1,n);              }
     tab=ivector(1,NCOVMAX);        }
     ncodemax=ivector(1,8);        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
     i=1;           as a weighted average of prlim.
     while (fgets(line, MAXLINE, fic) != NULL)    {        */
       if ((i >= firstobs) && (i <=lastobs)) {        for(j=nlstate+1;j<=nlstate+ndeath;j++){
                  for(i=1,gmp[j]=0.; i<= nlstate; i++)
         for (j=maxwav;j>=1;j--){           gmp[j] += prlim[i][i]*p3mat[i][j][1];
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        }    
           strcpy(line,stra);        /* end probability of death */
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        for(j=1; j<= nlstate; j++) /* vareij */
         }          for(h=0; h<=nhstepm; h++){
                    gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);          }
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        }
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      } /* End theta */
         for (j=ncovcol;j>=1;j--){  
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
         }  
         num[i]=atol(stra);      for(h=0; h<=nhstepm; h++) /* veij */
                for(j=1; j<=nlstate;j++)
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          for(theta=1; theta <=npar; theta++)
           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;}*/            trgradg[h][j][theta]=gradg[h][theta][j];
   
         i=i+1;      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       }        for(theta=1; theta <=npar; theta++)
     }          trgradgp[j][theta]=gradgp[theta][j];
     /* printf("ii=%d", ij);    
        scanf("%d",i);*/  
   imx=i-1; /* Number of individuals */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
   /* for (i=1; i<=imx; i++){        for(j=1;j<=nlstate;j++)
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          vareij[i][j][(int)age] =0.;
     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(h=0;h<=nhstepm;h++){
     }*/        for(k=0;k<=nhstepm;k++){
    /*  for (i=1; i<=imx; i++){          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
      if (s[4][i]==9)  s[4][i]=-1;          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
      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(i=1;i<=nlstate;i++)
              for(j=1;j<=nlstate;j++)
                vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   /* Calculation of the number of parameter from char model*/        }
   Tvar=ivector(1,15);      }
   Tprod=ivector(1,15);    
   Tvaraff=ivector(1,15);      /* pptj */
   Tvard=imatrix(1,15,1,2);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   Tage=ivector(1,15);            matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
          for(j=nlstate+1;j<=nlstate+ndeath;j++)
   if (strlen(model) >1){        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     j=0, j1=0, k1=1, k2=1;          varppt[j][i]=doldmp[j][i];
     j=nbocc(model,'+');      /* end ppptj */
     j1=nbocc(model,'*');      /*  x centered again */
     cptcovn=j+1;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     cptcovprod=j1;      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
       
     strcpy(modelsav,model);      if (popbased==1) {
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        if(mobilav ==0){
       printf("Error. Non available option model=%s ",model);          for(i=1; i<=nlstate;i++)
       goto end;            prlim[i][i]=probs[(int)age][i][ij];
     }        }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
     for(i=(j+1); i>=1;i--){            prlim[i][i]=mobaverage[(int)age][i][ij];
       cutv(stra,strb,modelsav,'+');        }
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      }
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/               
       /*scanf("%d",i);*/      /* This for computing probability of death (h=1 means
       if (strchr(strb,'*')) {         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         cutv(strd,strc,strb,'*');         as a weighted average of prlim.
         if (strcmp(strc,"age")==0) {      */
           cptcovprod--;      for(j=nlstate+1;j<=nlstate+ndeath;j++){
           cutv(strb,stre,strd,'V');        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           Tvar[i]=atoi(stre);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           cptcovage++;      }    
             Tage[cptcovage]=i;      /* end probability of death */
             /*printf("stre=%s ", stre);*/  
         }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
         else if (strcmp(strd,"age")==0) {      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           cptcovprod--;        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
           cutv(strb,stre,strc,'V');        for(i=1; i<=nlstate;i++){
           Tvar[i]=atoi(stre);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
           cptcovage++;        }
           Tage[cptcovage]=i;      } 
         }      fprintf(ficresprobmorprev,"\n");
         else {  
           cutv(strb,stre,strc,'V');      fprintf(ficresvij,"%.0f ",age );
           Tvar[i]=ncovcol+k1;      for(i=1; i<=nlstate;i++)
           cutv(strb,strc,strd,'V');        for(j=1; j<=nlstate;j++){
           Tprod[k1]=i;          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
           Tvard[k1][1]=atoi(strc);        }
           Tvard[k1][2]=atoi(stre);      fprintf(ficresvij,"\n");
           Tvar[cptcovn+k2]=Tvard[k1][1];      free_matrix(gp,0,nhstepm,1,nlstate);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      free_matrix(gm,0,nhstepm,1,nlstate);
           for (k=1; k<=lastobs;k++)      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
           k1++;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           k2=k2+2;    } /* End age */
         }    free_vector(gpp,nlstate+1,nlstate+ndeath);
       }    free_vector(gmp,nlstate+1,nlstate+ndeath);
       else {    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
        /*  scanf("%d",i);*/    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
       cutv(strd,strc,strb,'V');    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       Tvar[i]=atoi(strc);    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); */
       strcpy(modelsav,stra);    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
         scanf("%d",i);*/    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));
 }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
      fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    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);
   printf("cptcovprod=%d ", cptcovprod);    /*  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);
   scanf("%d ",i);*/  */
     fclose(fic);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/    free_vector(xp,1,npar);
       for(i=1;i<=n;i++) weight[i]=1.0;    free_matrix(doldm,1,nlstate,1,nlstate);
     }    free_matrix(dnewm,1,nlstate,1,npar);
     /*-calculation of age at interview from date of interview and age at death -*/    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     agev=matrix(1,maxwav,1,imx);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     for (i=1; i<=imx; i++) {    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(m=2; (m<= maxwav); m++) {    fclose(ficresprobmorprev);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    fflush(ficgp);
          anint[m][i]=9999;    fflush(fichtm); 
          s[m][i]=-1;  }  /* end varevsij */
        }  
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;  /************ 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, char strstart[])
     }  {
     /* Variance of prevalence limit */
     for (i=1; i<=imx; i++)  {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    double **newm;
       for(m=1; (m<= maxwav); m++){    double **dnewm,**doldm;
         if(s[m][i] >0){    int i, j, nhstepm, hstepm;
           if (s[m][i] >= nlstate+1) {    int k, cptcode;
             if(agedc[i]>0)    double *xp;
               if(moisdc[i]!=99 && andc[i]!=9999)    double *gp, *gm;
                 agev[m][i]=agedc[i];    double **gradg, **trgradg;
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    double age,agelim;
            else {    int theta;
               if (andc[i]!=9999){    
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    pstamp(ficresvpl);
               agev[m][i]=-1;    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
               }    fprintf(ficresvpl,"# Age");
             }    for(i=1; i<=nlstate;i++)
           }        fprintf(ficresvpl," %1d-%1d",i,i);
           else if(s[m][i] !=9){ /* Should no more exist */    fprintf(ficresvpl,"\n");
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  
             if(mint[m][i]==99 || anint[m][i]==9999)    xp=vector(1,npar);
               agev[m][i]=1;    dnewm=matrix(1,nlstate,1,npar);
             else if(agev[m][i] <agemin){    doldm=matrix(1,nlstate,1,nlstate);
               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);*/    hstepm=1*YEARM; /* Every year of age */
             }    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
             else if(agev[m][i] >agemax){    agelim = AGESUP;
               agemax=agev[m][i];    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             }      if (stepm >= YEARM) hstepm=1;
             /*agev[m][i]=anint[m][i]-annais[i];*/      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
             /*   agev[m][i] = age[i]+2*m;*/      gradg=matrix(1,npar,1,nlstate);
           }      gp=vector(1,nlstate);
           else { /* =9 */      gm=vector(1,nlstate);
             agev[m][i]=1;  
             s[m][i]=-1;      for(theta=1; theta <=npar; theta++){
           }        for(i=1; i<=npar; i++){ /* Computes gradient */
         }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         else /*= 0 Unknown */        }
           agev[m][i]=1;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       }        for(i=1;i<=nlstate;i++)
              gp[i] = prlim[i][i];
     }      
     for (i=1; i<=imx; i++)  {        for(i=1; i<=npar; i++) /* Computes gradient */
       for(m=1; (m<= maxwav); m++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         if (s[m][i] > (nlstate+ndeath)) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           printf("Error: Wrong value in nlstate or ndeath\n");          for(i=1;i<=nlstate;i++)
           goto end;          gm[i] = prlim[i][i];
         }  
       }        for(i=1;i<=nlstate;i++)
     }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  
       trgradg =matrix(1,nlstate,1,npar);
     free_vector(severity,1,maxwav);  
     free_imatrix(outcome,1,maxwav+1,1,n);      for(j=1; j<=nlstate;j++)
     free_vector(moisnais,1,n);        for(theta=1; theta <=npar; theta++)
     free_vector(annais,1,n);          trgradg[j][theta]=gradg[theta][j];
     /* free_matrix(mint,1,maxwav,1,n);  
        free_matrix(anint,1,maxwav,1,n);*/      for(i=1;i<=nlstate;i++)
     free_vector(moisdc,1,n);        varpl[i][(int)age] =0.;
     free_vector(andc,1,n);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
          for(i=1;i<=nlstate;i++)
     wav=ivector(1,imx);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      fprintf(ficresvpl,"%.0f ",age );
          for(i=1; i<=nlstate;i++)
     /* Concatenates waves */        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       Tcode=ivector(1,100);      free_matrix(gradg,1,npar,1,nlstate);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      free_matrix(trgradg,1,nlstate,1,npar);
       ncodemax[1]=1;    } /* End age */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  
          free_vector(xp,1,npar);
    codtab=imatrix(1,100,1,10);    free_matrix(doldm,1,nlstate,1,npar);
    h=0;    free_matrix(dnewm,1,nlstate,1,nlstate);
    m=pow(2,cptcoveff);  
    }
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){  /************ Variance of one-step probabilities  ******************/
        for(j=1; j <= ncodemax[k]; j++){  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[])
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  {
            h++;    int i, j=0,  i1, k1, l1, t, tj;
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    int k2, l2, j1,  z1;
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    int k=0,l, cptcode;
          }    int first=1, first1;
        }    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
      }    double **dnewm,**doldm;
    }    double *xp;
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    double *gp, *gm;
       codtab[1][2]=1;codtab[2][2]=2; */    double **gradg, **trgradg;
    /* for(i=1; i <=m ;i++){    double **mu;
       for(k=1; k <=cptcovn; k++){    double age,agelim, cov[NCOVMAX];
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
       }    int theta;
       printf("\n");    char fileresprob[FILENAMELENGTH];
       }    char fileresprobcov[FILENAMELENGTH];
       scanf("%d",i);*/    char fileresprobcor[FILENAMELENGTH];
      
    /* Calculates basic frequencies. Computes observed prevalence at single age    double ***varpij;
        and prints on file fileres'p'. */  
     strcpy(fileresprob,"prob"); 
        strcat(fileresprob,fileres);
        if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      printf("Problem with resultfile: %s\n", fileresprob);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    strcpy(fileresprobcov,"probcov"); 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    strcat(fileresprobcov,fileres);
          if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     /* For Powell, parameters are in a vector p[] starting at p[1]      printf("Problem with resultfile: %s\n", fileresprobcov);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    }
     strcpy(fileresprobcor,"probcor"); 
     if(mle==1){    strcat(fileresprobcor,fileres);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     }      printf("Problem with resultfile: %s\n", fileresprobcor);
          fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     /*--------- 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);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
      fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
    jk=1;    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
    for(i=1,jk=1; i <=nlstate; i++){    pstamp(ficresprob);
      for(k=1; k <=(nlstate+ndeath); k++){    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
        if (k != i)    fprintf(ficresprob,"# Age");
          {    pstamp(ficresprobcov);
            printf("%d%d ",i,k);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
            fprintf(ficres,"%1d%1d ",i,k);    fprintf(ficresprobcov,"# Age");
            for(j=1; j <=ncovmodel; j++){    pstamp(ficresprobcor);
              printf("%f ",p[jk]);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
              fprintf(ficres,"%f ",p[jk]);    fprintf(ficresprobcor,"# Age");
              jk++;  
            }  
            printf("\n");    for(i=1; i<=nlstate;i++)
            fprintf(ficres,"\n");      for(j=1; j<=(nlstate+ndeath);j++){
          }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
      }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
    }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
  if(mle==1){      }  
     /* Computing hessian and covariance matrix */   /* fprintf(ficresprob,"\n");
     ftolhess=ftol; /* Usually correct */    fprintf(ficresprobcov,"\n");
     hesscov(matcov, p, npar, delti, ftolhess, func);    fprintf(ficresprobcor,"\n");
  }   */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");   xp=vector(1,npar);
     printf("# Scales (for hessian or gradient estimation)\n");    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      for(i=1,jk=1; i <=nlstate; i++){    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       for(j=1; j <=nlstate+ndeath; j++){    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
         if (j!=i) {    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
           fprintf(ficres,"%1d%1d",i,j);    first=1;
           printf("%1d%1d",i,j);    fprintf(ficgp,"\n# Routine varprob");
           for(k=1; k<=ncovmodel;k++){    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
             printf(" %.5e",delti[jk]);    fprintf(fichtm,"\n");
             fprintf(ficres," %.5e",delti[jk]);  
             jk++;    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
           }    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
           printf("\n");    file %s<br>\n",optionfilehtmcov);
           fprintf(ficres,"\n");    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
         }  and drawn. It helps understanding how is the covariance between two incidences.\
       }   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
      }    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
      It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
     k=1;  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
     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");  standard deviations wide on each axis. <br>\
     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");   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
     for(i=1;i<=npar;i++){   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
       /*  if (k>nlstate) k=1;  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
       i1=(i-1)/(ncovmodel*nlstate)+1;  
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    cov[1]=1;
       printf("%s%d%d",alph[k],i1,tab[i]);*/    tj=cptcoveff;
       fprintf(ficres,"%3d",i);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
       printf("%3d",i);    j1=0;
       for(j=1; j<=i;j++){    for(t=1; t<=tj;t++){
         fprintf(ficres," %.5e",matcov[i][j]);      for(i1=1; i1<=ncodemax[t];i1++){ 
         printf(" %.5e",matcov[i][j]);        j1++;
       }        if  (cptcovn>0) {
       fprintf(ficres,"\n");          fprintf(ficresprob, "\n#********** Variable "); 
       printf("\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       k++;          fprintf(ficresprob, "**********\n#\n");
     }          fprintf(ficresprobcov, "\n#********** Variable "); 
              for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresprobcov, "**********\n#\n");
       ungetc(c,ficpar);          
       fgets(line, MAXLINE, ficpar);          fprintf(ficgp, "\n#********** Variable "); 
       puts(line);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fputs(line,ficparo);          fprintf(ficgp, "**********\n#\n");
     }          
     ungetc(c,ficpar);          
     estepm=0;          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     if (estepm==0 || estepm < stepm) estepm=stepm;          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     if (fage <= 2) {          
       bage = ageminpar;          fprintf(ficresprobcor, "\n#********** Variable ");    
       fage = agemaxpar;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     }          fprintf(ficresprobcor, "**********\n#");    
            }
     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);        for (age=bage; age<=fage; age ++){ 
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);          cov[2]=age;
            for (k=1; k<=cptcovn;k++) {
     while((c=getc(ficpar))=='#' && c!= EOF){            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     puts(line);          for (k=1; k<=cptcovprod;k++)
     fputs(line,ficparo);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   }          
   ungetc(c,ficpar);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
            trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);          gp=vector(1,(nlstate)*(nlstate+ndeath));
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          gm=vector(1,(nlstate)*(nlstate+ndeath));
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      
                for(theta=1; theta <=npar; theta++){
   while((c=getc(ficpar))=='#' && c!= EOF){            for(i=1; i<=npar; i++)
     ungetc(c,ficpar);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     fgets(line, MAXLINE, ficpar);            
     puts(line);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     fputs(line,ficparo);            
   }            k=0;
   ungetc(c,ficpar);            for(i=1; i<= (nlstate); i++){
                for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                gp[k]=pmmij[i][j];
    dateprev2=anprev2+mprev2/12.+jprev2/365.;              }
             }
   fscanf(ficpar,"pop_based=%d\n",&popbased);            
   fprintf(ficparo,"pop_based=%d\n",popbased);              for(i=1; i<=npar; i++)
   fprintf(ficres,"pop_based=%d\n",popbased);                xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
        
   while((c=getc(ficpar))=='#' && c!= EOF){            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     ungetc(c,ficpar);            k=0;
     fgets(line, MAXLINE, ficpar);            for(i=1; i<=(nlstate); i++){
     puts(line);              for(j=1; j<=(nlstate+ndeath);j++){
     fputs(line,ficparo);                k=k+1;
   }                gm[k]=pmmij[i][j];
   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);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
 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);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
 while((c=getc(ficpar))=='#' && c!= EOF){          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     ungetc(c,ficpar);            for(theta=1; theta <=npar; theta++)
     fgets(line, MAXLINE, ficpar);              trgradg[j][theta]=gradg[theta][j];
     puts(line);          
     fputs(line,ficparo);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   }          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   ungetc(c,ficpar);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  
           pmij(pmmij,cov,ncovmodel,x,nlstate);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          
           k=0;
 /*------------ gnuplot -------------*/          for(i=1; i<=(nlstate); i++){
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);            for(j=1; j<=(nlstate+ndeath);j++){
                k=k+1;
 /*------------ free_vector  -------------*/              mu[k][(int) age]=pmmij[i][j];
  chdir(path);            }
            }
  free_ivector(wav,1,imx);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                varpij[i][j][(int)age] = doldm[i][j];
  free_ivector(num,1,n);  
  free_vector(agedc,1,n);          /*printf("\n%d ",(int)age);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
  fclose(ficparo);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
  fclose(ficres);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
 /*--------- index.htm --------*/  
           fprintf(ficresprob,"\n%d ",(int)age);
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);          fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
    
   /*--------------- Prevalence limit --------------*/          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
              fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   strcpy(filerespl,"pl");          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   strcat(filerespl,fileres);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          }
   }          i=0;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          for (k=1; k<=(nlstate);k++){
   fprintf(ficrespl,"#Prevalence limit\n");            for (l=1; l<=(nlstate+ndeath);l++){ 
   fprintf(ficrespl,"#Age ");              i=i++;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   fprintf(ficrespl,"\n");              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                for (j=1; j<=i;j++){
   prlim=matrix(1,nlstate,1,nlstate);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   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 */          }/* end of loop for state */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        } /* end of loop for age */
   k=0;  
   agebase=ageminpar;        /* Confidence intervalle of pij  */
   agelim=agemaxpar;        /*
   ftolpl=1.e-10;          fprintf(ficgp,"\nset noparametric;unset label");
   i1=cptcoveff;          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   if (cptcovn < 1){i1=1;}          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(cptcov=1;cptcov<=i1;cptcov++){          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
         k=k+1;          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        */
         fprintf(ficrespl,"\n#******");  
         for(j=1;j<=cptcoveff;j++)        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        first1=1;
         fprintf(ficrespl,"******\n");        for (k2=1; k2<=(nlstate);k2++){
                  for (l2=1; l2<=(nlstate+ndeath);l2++){ 
         for (age=agebase; age<=agelim; age++){            if(l2==k2) continue;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            j=(k2-1)*(nlstate+ndeath)+l2;
           fprintf(ficrespl,"%.0f",age );            for (k1=1; k1<=(nlstate);k1++){
           for(i=1; i<=nlstate;i++)              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
           fprintf(ficrespl," %.5f", prlim[i][i]);                if(l1==k1) continue;
           fprintf(ficrespl,"\n");                i=(k1-1)*(nlstate+ndeath)+l1;
         }                if(i<=j) continue;
       }                for (age=bage; age<=fage; age ++){ 
     }                  if ((int)age %5==0){
   fclose(ficrespl);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   /*------------- h Pij x at various ages ------------*/                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                      mu1=mu[i][(int) age]/stepm*YEARM ;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);                    mu2=mu[j][(int) age]/stepm*YEARM;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                    c12=cv12/sqrt(v1*v2);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                    /* Computing eigen value of matrix of covariance */
   }                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   printf("Computing pij: result on file '%s' \n", filerespij);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                      /* Eigen vectors */
   stepsize=(int) (stepm+YEARM-1)/YEARM;                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
   /*if (stepm<=24) stepsize=2;*/                    /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
   agelim=AGESUP;                    v12=-v21;
   hstepm=stepsize*YEARM; /* Every year of age */                    v22=v11;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */                    tnalp=v21/v11;
                      if(first1==1){
   k=0;                      first1=0;
   for(cptcov=1;cptcov<=i1;cptcov++){                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    }
       k=k+1;                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
         fprintf(ficrespij,"\n#****** ");                    /*printf(fignu*/
         for(j=1;j<=cptcoveff;j++)                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
         fprintf(ficrespij,"******\n");                    if(first==1){
                              first=0;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                      fprintf(ficgp,"\nset parametric;unset label");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                      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);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
           oldm=oldms;savm=savms;   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
           fprintf(ficrespij,"# Age");                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
           for(i=1; i<=nlstate;i++)                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
             for(j=1; j<=nlstate+ndeath;j++)                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
               fprintf(ficrespij," %1d-%1d",i,j);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
           fprintf(ficrespij,"\n");                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
            for (h=0; h<=nhstepm; h++){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
             for(i=1; i<=nlstate;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",\
               for(j=1; j<=nlstate+ndeath;j++)                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
             fprintf(ficrespij,"\n");                    }else{
              }                      first=0;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
           fprintf(ficrespij,"\n");                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
         }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     }                      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));
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);                    }/* if first */
                   } /* age mod 5 */
   fclose(ficrespij);                } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
   /*---------- Forecasting ------------------*/              } /*l12 */
   if((stepm == 1) && (strcmp(model,".")==0)){            } /* k12 */
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);          } /*l1 */
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);        }/* k1 */
   }      } /* loop covariates */
   else{    }
     erreur=108;    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     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);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   }    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
   /*---------- Health expectancies and variances ------------*/    fclose(ficresprob);
     fclose(ficresprobcov);
   strcpy(filerest,"t");    fclose(ficresprobcor);
   strcat(filerest,fileres);    fflush(ficgp);
   if((ficrest=fopen(filerest,"w"))==NULL) {    fflush(fichtmcov);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  }
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   strcpy(filerese,"e");                    int lastpass, int stepm, int weightopt, char model[],\
   strcat(filerese,fileres);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   if((ficreseij=fopen(filerese,"w"))==NULL) {                    int popforecast, int estepm ,\
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);                    double jprev1, double mprev1,double anprev1, \
   }                    double jprev2, double mprev2,double anprev2){
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    int jj1, k1, i1, cpt;
   
  strcpy(fileresv,"v");     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
   strcat(fileresv,fileres);     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  </ul>");
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
   }   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
   calagedate=-1;     fprintf(fichtm,"\
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
   k=0;     fprintf(fichtm,"\
   for(cptcov=1;cptcov<=i1;cptcov++){   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
       k=k+1;     fprintf(fichtm,"\
       fprintf(ficrest,"\n#****** ");   - (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): \
       for(j=1;j<=cptcoveff;j++)     <a href=\"%s\">%s</a> <br>\n</li>",
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
       fprintf(ficrest,"******\n");  
   
       fprintf(ficreseij,"\n#****** ");  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   m=cptcoveff;
       fprintf(ficreseij,"******\n");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
       fprintf(ficresvij,"\n#****** ");   jj1=0;
       for(j=1;j<=cptcoveff;j++)   for(k1=1; k1<=m;k1++){
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     for(i1=1; i1<=ncodemax[k1];i1++){
       fprintf(ficresvij,"******\n");       jj1++;
        if (cptcovn > 0) {
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       oldm=oldms;savm=savms;         for (cpt=1; cpt<=cptcoveff;cpt++) 
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);             fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);       }
       oldm=oldms;savm=savms;       /* Pij */
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);       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> \
      <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
         fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");   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> \
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
       fprintf(ficrest,"\n");         /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
       epj=vector(1,nlstate+1);           fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
       for(age=bage; age <=fage ;age++){  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);         }
         if (popbased==1) {       for(cpt=1; cpt<=nlstate;cpt++) {
           for(i=1; i<=nlstate;i++)          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> \
             prlim[i][i]=probs[(int)age][i][k];  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
         }       }
             } /* end i1 */
         fprintf(ficrest," %4.0f",age);   }/* End k1 */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){   fprintf(fichtm,"</ul>");
           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]);*/   fprintf(fichtm,"\
           }  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
           epj[nlstate+1] +=epj[j];   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
         }  
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
         for(i=1, vepp=0.;i <=nlstate;i++)           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
           for(j=1;j <=nlstate;j++)   fprintf(fichtm,"\
             vepp += vareij[i][j][(int)age];   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
         for(j=1;j <=nlstate;j++){  
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));   fprintf(fichtm,"\
         }   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
         fprintf(ficrest,"\n");           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
       }   fprintf(fichtm,"\
     }   - 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): \
   }     <a href=\"%s\">%s</a> <br>\n</li>",
 free_matrix(mint,1,maxwav,1,n);             estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);   fprintf(fichtm,"\
     free_vector(weight,1,n);   - (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): \
   fclose(ficreseij);     <a href=\"%s\">%s</a> <br>\n</li>",
   fclose(ficresvij);             estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
   fclose(ficrest);   fprintf(fichtm,"\
   fclose(ficpar);   - 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",
   free_vector(epj,1,nlstate+1);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
     fprintf(fichtm,"\
   /*------- Variance limit prevalence------*/     - 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",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
   strcpy(fileresvpl,"vpl");   fprintf(fichtm,"\
   strcat(fileresvpl,fileres);   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  
     exit(0);  /*  if(popforecast==1) fprintf(fichtm,"\n */
   }  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   k=0;  /*  else  */
   for(cptcov=1;cptcov<=i1;cptcov++){  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   fflush(fichtm);
       k=k+1;   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
       fprintf(ficresvpl,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)   m=cptcoveff;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       fprintf(ficresvpl,"******\n");  
         jj1=0;
       varpl=matrix(1,nlstate,(int) bage, (int) fage);   for(k1=1; k1<=m;k1++){
       oldm=oldms;savm=savms;     for(i1=1; i1<=ncodemax[k1];i1++){
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);       jj1++;
     }       if (cptcovn > 0) {
  }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
   fclose(ficresvpl);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   /*---------- End : free ----------------*/       }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);       for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
         }
         fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  health expectancies in states (1) and (2): %s%d.png<br>\
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);     } /* end i1 */
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);   }/* End k1 */
     fprintf(fichtm,"</ul>");
   free_matrix(matcov,1,npar,1,npar);   fflush(fichtm);
   free_vector(delti,1,npar);  }
   free_matrix(agev,1,maxwav,1,imx);  
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   if(erreur >0)  
     printf("End of Imach with error or warning %d\n",erreur);    char dirfileres[132],optfileres[132];
   else   printf("End of Imach\n");    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    int ng;
    /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/  /*     printf("Problem with file %s",optionfilegnuplot); */
   /*printf("Total time was %d uSec.\n", total_usecs);*/  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*------ End -----------*/  /*   } */
   
     /*#ifdef windows */
  end:    fprintf(ficgp,"cd \"%s\" \n",pathc);
 #ifdef windows      /*#endif */
   /* chdir(pathcd);*/    m=pow(2,cptcoveff);
 #endif  
  /*system("wgnuplot graph.plt");*/    strcpy(dirfileres,optionfilefiname);
  /*system("../gp37mgw/wgnuplot graph.plt");*/    strcpy(optfileres,"vpl");
  /*system("cd ../gp37mgw");*/   /* 1eme*/
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    for (cpt=1; cpt<= nlstate ; cpt ++) {
  strcpy(plotcmd,GNUPLOTPROGRAM);     for (k1=1; k1<= m ; k1 ++) {
  strcat(plotcmd," ");       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
  strcat(plotcmd,optionfilegnuplot);       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
  system(plotcmd);       fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
 #ifdef windows  set ter png small\n\
   while (z[0] != 'q') {  set size 0.65,0.65\n\
     /* chdir(path); */  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");  
     scanf("%s",z);       for (i=1; i<= nlstate ; i ++) {
     if (z[0] == 'c') system("./imach");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     else if (z[0] == 'e') system(optionfilehtm);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     else if (z[0] == 'g') system(plotcmd);       }
     else if (z[0] == 'q') exit(0);       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 ++) {
 #endif         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
 }         else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+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(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         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.1.46  
changed lines
  Added in v.1.122


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