Diff for /imach/src/imach.c between versions 1.35 and 1.131

version 1.35, 2002/03/26 17:08:39 version 1.131, 2009/06/20 16:22:47
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.131  2009/06/20 16:22:47  brouard
      Some dimensions resccaled
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.130  2009/05/26 06:44:34  brouard
   first survey ("cross") where individuals from different ages are    (Module): Max Covariate is now set to 20 instead of 8. A
   interviewed on their health status or degree of disability (in the    lot of cleaning with variables initialized to 0. Trying to make
   case of a health survey which is our main interest) -2- at least a    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.129  2007/08/31 13:49:27  lievre
   computed from the time spent in each health state according to a    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.128  2006/06/30 13:02:05  brouard
   simplest model is the multinomial logistic model where pij is the    (Module): Clarifications on computing e.j
   probabibility to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.127  2006/04/28 18:11:50  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    (Module): Yes the sum of survivors was wrong since
   'age' is age and 'sex' is a covariate. If you want to have a more    imach-114 because nhstepm was no more computed in the age
   complex model than "constant and age", you should modify the program    loop. Now we define nhstepma in the age loop.
   where the markup *Covariates have to be included here again* invites    (Module): In order to speed up (in case of numerous covariates) we
   you to do it.  More covariates you add, slower the    compute health expectancies (without variances) in a first step
   convergence.    and then all the health expectancies with variances or standard
     deviation (needs data from the Hessian matrices) which slows the
   The advantage of this computer programme, compared to a simple    computation.
   multinomial logistic model, is clear when the delay between waves is not    In the future we should be able to stop the program is only health
   identical for each individual. Also, if a individual missed an    expectancies and graph are needed without standard deviations.
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.126  2006/04/28 17:23:28  brouard
     (Module): Yes the sum of survivors was wrong since
   hPijx is the probability to be observed in state i at age x+h    imach-114 because nhstepm was no more computed in the age
   conditional to the observed state i at age x. The delay 'h' can be    loop. Now we define nhstepma in the age loop.
   split into an exact number (nh*stepm) of unobserved intermediate    Version 0.98h
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.125  2006/04/04 15:20:31  lievre
   matrix is simply the matrix product of nh*stepm elementary matrices    Errors in calculation of health expectancies. Age was not initialized.
   and the contribution of each individual to the likelihood is simply    Forecasting file added.
   hPijx.  
     Revision 1.124  2006/03/22 17:13:53  lievre
   Also this programme outputs the covariance matrix of the parameters but also    Parameters are printed with %lf instead of %f (more numbers after the comma).
   of the life expectancies. It also computes the prevalence limits.    The log-likelihood is printed in the log file
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.123  2006/03/20 10:52:43  brouard
            Institut national d'études démographiques, Paris.    * imach.c (Module): <title> changed, corresponds to .htm file
   This software have been partly granted by Euro-REVES, a concerted action    name. <head> headers where missing.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    * imach.c (Module): Weights can have a decimal point as for
   software can be distributed freely for non commercial use. Latest version    English (a comma might work with a correct LC_NUMERIC environment,
   can be accessed at http://euroreves.ined.fr/imach .    otherwise the weight is truncated).
   **********************************************************************/    Modification of warning when the covariates values are not 0 or
      1.
 #include <math.h>    Version 0.98g
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.122  2006/03/20 09:45:41  brouard
 #include <unistd.h>    (Module): Weights can have a decimal point as for
     English (a comma might work with a correct LC_NUMERIC environment,
 #define MAXLINE 256    otherwise the weight is truncated).
 #define GNUPLOTPROGRAM "wgnuplot"    Modification of warning when the covariates values are not 0 or
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    1.
 #define FILENAMELENGTH 80    Version 0.98g
 /*#define DEBUG*/  
 #define windows    Revision 1.121  2006/03/16 17:45:01  lievre
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    * imach.c (Module): Comments concerning covariates added
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     * imach.c (Module): refinements in the computation of lli if
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    status=-2 in order to have more reliable computation if stepm is
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    not 1 month. Version 0.98f
   
 #define NINTERVMAX 8    Revision 1.120  2006/03/16 15:10:38  lievre
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    (Module): refinements in the computation of lli if
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    status=-2 in order to have more reliable computation if stepm is
 #define NCOVMAX 8 /* Maximum number of covariates */    not 1 month. Version 0.98f
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.119  2006/03/15 17:42:26  brouard
 #define AGESUP 130    (Module): Bug if status = -2, the loglikelihood was
 #define AGEBASE 40    computed as likelihood omitting the logarithm. Version O.98e
   
     Revision 1.118  2006/03/14 18:20:07  brouard
 int erreur; /* Error number */    (Module): varevsij Comments added explaining the second
 int nvar;    table of variances if popbased=1 .
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int npar=NPARMAX;    (Module): Function pstamp added
 int nlstate=2; /* Number of live states */    (Module): Version 0.98d
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.117  2006/03/14 17:16:22  brouard
 int popbased=0;    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
 int *wav; /* Number of waves for this individuual 0 is possible */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int maxwav; /* Maxim number of waves */    (Module): Function pstamp added
 int jmin, jmax; /* min, max spacing between 2 waves */    (Module): Version 0.98d
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Revision 1.116  2006/03/06 10:29:27  brouard
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    (Module): Variance-covariance wrong links and
 double jmean; /* Mean space between 2 waves */    varian-covariance of ej. is needed (Saito).
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Revision 1.115  2006/02/27 12:17:45  brouard
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    (Module): One freematrix added in mlikeli! 0.98c
 FILE *ficgp,*ficresprob,*ficpop;  
 FILE *ficreseij;    Revision 1.114  2006/02/26 12:57:58  brouard
   char filerese[FILENAMELENGTH];    (Module): Some improvements in processing parameter
  FILE  *ficresvij;    filename with strsep.
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.113  2006/02/24 14:20:24  brouard
   char fileresvpl[FILENAMELENGTH];    (Module): Memory leaks checks with valgrind and:
     datafile was not closed, some imatrix were not freed and on matrix
 #define NR_END 1    allocation too.
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.112  2006/01/30 09:55:26  brouard
     (Module): Back to gnuplot.exe instead of wgnuplot.exe
 #define NRANSI  
 #define ITMAX 200    Revision 1.111  2006/01/25 20:38:18  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 #define TOL 2.0e-4    (Module): Comments can be added in data file. Missing date values
     can be a simple dot '.'.
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.110  2006/01/25 00:51:50  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    (Module): Lots of cleaning and bugs added (Gompertz)
   
 #define GOLD 1.618034    Revision 1.109  2006/01/24 19:37:15  brouard
 #define GLIMIT 100.0    (Module): Comments (lines starting with a #) are allowed in data.
 #define TINY 1.0e-20  
     Revision 1.108  2006/01/19 18:05:42  lievre
 static double maxarg1,maxarg2;    Gnuplot problem appeared...
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    To be fixed
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.107  2006/01/19 16:20:37  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Test existence of gnuplot in imach path
 #define rint(a) floor(a+0.5)  
     Revision 1.106  2006/01/19 13:24:36  brouard
 static double sqrarg;    Some cleaning and links added in html output
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Revision 1.105  2006/01/05 20:23:19  lievre
     *** empty log message ***
 int imx;  
 int stepm;    Revision 1.104  2005/09/30 16:11:43  lievre
 /* Stepm, step in month: minimum step interpolation*/    (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
 int m,nb;    that the person is alive, then we can code his/her status as -2
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    (instead of missing=-1 in earlier versions) and his/her
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    contributions to the likelihood is 1 - Prob of dying from last
 double **pmmij, ***probs, ***mobaverage;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 double dateintmean=0;    the healthy state at last known wave). Version is 0.98
   
 double *weight;    Revision 1.103  2005/09/30 15:54:49  lievre
 int **s; /* Status */    (Module): sump fixed, loop imx fixed, and simplifications.
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.102  2004/09/15 17:31:30  brouard
     Add the possibility to read data file including tab characters.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.101  2004/09/15 10:38:38  brouard
     Fix on curr_time
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Revision 1.100  2004/07/12 18:29:06  brouard
 {    Add version for Mac OS X. Just define UNIX in Makefile
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.98  2004/05/16 15:05:56  brouard
 #ifdef windows    New version 0.97 . First attempt to estimate force of mortality
    s = strrchr( path, '\\' );           /* find last / */    directly from the data i.e. without the need of knowing the health
 #else    state at each age, but using a Gompertz model: log u =a + b*age .
    s = strrchr( path, '/' );            /* find last / */    This is the basic analysis of mortality and should be done before any
 #endif    other analysis, in order to test if the mortality estimated from the
    if ( s == NULL ) {                   /* no directory, so use current */    cross-longitudinal survey is different from the mortality estimated
 #if     defined(__bsd__)                /* get current working directory */    from other sources like vital statistic data.
       extern char       *getwd( );  
     The same imach parameter file can be used but the option for mle should be -3.
       if ( getwd( dirc ) == NULL ) {  
 #else    Agnès, who wrote this part of the code, tried to keep most of the
       extern char       *getcwd( );    former routines in order to include the new code within the former code.
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    The output is very simple: only an estimate of the intercept and of
 #endif    the slope with 95% confident intervals.
          return( GLOCK_ERROR_GETCWD );  
       }    Current limitations:
       strcpy( name, path );             /* we've got it */    A) Even if you enter covariates, i.e. with the
    } else {                             /* strip direcotry from path */    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
       s++;                              /* after this, the filename */    B) There is no computation of Life Expectancy nor Life Table.
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.97  2004/02/20 13:25:42  lievre
       strcpy( name, s );                /* save file name */    Version 0.96d. Population forecasting command line is (temporarily)
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    suppressed.
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.96  2003/07/15 15:38:55  brouard
    l1 = strlen( dirc );                 /* length of directory */    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #ifdef windows    rewritten within the same printf. Workaround: many printfs.
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else    Revision 1.95  2003/07/08 07:54:34  brouard
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    * imach.c (Repository):
 #endif    (Repository): Using imachwizard code to output a more meaningful covariance
    s = strrchr( name, '.' );            /* find last / */    matrix (cov(a12,c31) instead of numbers.
    s++;  
    strcpy(ext,s);                       /* save extension */    Revision 1.94  2003/06/27 13:00:02  brouard
    l1= strlen( name);    Just cleaning
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);    Revision 1.93  2003/06/25 16:33:55  brouard
    finame[l1-l2]= 0;    (Module): On windows (cygwin) function asctime_r doesn't
    return( 0 );                         /* we're done */    exist so I changed back to asctime which exists.
 }    (Module): Version 0.96b
   
     Revision 1.92  2003/06/25 16:30:45  brouard
 /******************************************/    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 void replace(char *s, char*t)  
 {    Revision 1.91  2003/06/25 15:30:29  brouard
   int i;    * imach.c (Repository): Duplicated warning errors corrected.
   int lg=20;    (Repository): Elapsed time after each iteration is now output. It
   i=0;    helps to forecast when convergence will be reached. Elapsed time
   lg=strlen(t);    is stamped in powell.  We created a new html file for the graphs
   for(i=0; i<= lg; i++) {    concerning matrix of covariance. It has extension -cov.htm.
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Revision 1.90  2003/06/24 12:34:15  brouard
   }    (Module): Some bugs corrected for windows. Also, when
 }    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 int nbocc(char *s, char occ)  
 {    Revision 1.89  2003/06/24 12:30:52  brouard
   int i,j=0;    (Module): Some bugs corrected for windows. Also, when
   int lg=20;    mle=-1 a template is output in file "or"mypar.txt with the design
   i=0;    of the covariance matrix to be input.
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.88  2003/06/23 17:54:56  brouard
   if  (s[i] == occ ) j++;    * 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.
   }  
   return j;    Revision 1.87  2003/06/18 12:26:01  brouard
 }    Version 0.96
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.86  2003/06/17 20:04:08  brouard
 {    (Module): Change position of html and gnuplot routines and added
   int i,lg,j,p=0;    routine fileappend.
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    Revision 1.85  2003/06/17 13:12:43  brouard
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    * imach.c (Repository): Check when date of death was earlier that
   }    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
   lg=strlen(t);    was wrong (infinity). We still send an "Error" but patch by
   for(j=0; j<p; j++) {    assuming that the date of death was just one stepm after the
     (u[j] = t[j]);    interview.
   }    (Repository): Because some people have very long ID (first column)
      u[p]='\0';    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
    for(j=0; j<= lg; j++) {    truncation)
     if (j>=(p+1))(v[j-p-1] = t[j]);    (Repository): No more line truncation errors.
   }  
 }    Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
 /********************** nrerror ********************/    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
 void nrerror(char error_text[])    parcimony.
 {    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    Revision 1.83  2003/06/10 13:39:11  lievre
   exit(1);    *** empty log message ***
 }  
 /*********************** vector *******************/    Revision 1.82  2003/06/05 15:57:20  brouard
 double *vector(int nl, int nh)    Add log in  imach.c and  fullversion number is now printed.
 {  
   double *v;  */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  /*
   if (!v) nrerror("allocation failure in vector");     Interpolated Markov Chain
   return v-nl+NR_END;  
 }    Short summary of the programme:
     
 /************************ free vector ******************/    This program computes Healthy Life Expectancies from
 void free_vector(double*v, int nl, int nh)    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 {    first survey ("cross") where individuals from different ages are
   free((FREE_ARG)(v+nl-NR_END));    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
 /************************ivector *******************************/    (if any) in individual health status.  Health expectancies are
 int *ivector(long nl,long nh)    computed from the time spent in each health state according to a
 {    model. More health states you consider, more time is necessary to reach the
   int *v;    Maximum Likelihood of the parameters involved in the model.  The
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    simplest model is the multinomial logistic model where pij is the
   if (!v) nrerror("allocation failure in ivector");    probability to be observed in state j at the second wave
   return v-nl+NR_END;    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
     'age' is age and 'sex' is a covariate. If you want to have a more
 /******************free ivector **************************/    complex model than "constant and age", you should modify the program
 void free_ivector(int *v, long nl, long nh)    where the markup *Covariates have to be included here again* invites
 {    you to do it.  More covariates you add, slower the
   free((FREE_ARG)(v+nl-NR_END));    convergence.
 }  
     The advantage of this computer programme, compared to a simple
 /******************* imatrix *******************************/    multinomial logistic model, is clear when the delay between waves is not
 int **imatrix(long nrl, long nrh, long ncl, long nch)    identical for each individual. Also, if a individual missed an
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    intermediate interview, the information is lost, but taken into
 {    account using an interpolation or extrapolation.  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    hPijx is the probability to be observed in state i at age x+h
      conditional to the observed state i at age x. The delay 'h' can be
   /* allocate pointers to rows */    split into an exact number (nh*stepm) of unobserved intermediate
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    states. This elementary transition (by month, quarter,
   if (!m) nrerror("allocation failure 1 in matrix()");    semester or year) is modelled as a multinomial logistic.  The hPx
   m += NR_END;    matrix is simply the matrix product of nh*stepm elementary matrices
   m -= nrl;    and the contribution of each individual to the likelihood is simply
      hPijx.
    
   /* allocate rows and set pointers to them */    Also this programme outputs the covariance matrix of the parameters but also
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    of the life expectancies. It also computes the period (stable) prevalence. 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    
   m[nrl] += NR_END;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   m[nrl] -= ncl;             Institut national d'études démographiques, Paris.
      This software have been partly granted by Euro-REVES, a concerted action
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    from the European Union.
      It is copyrighted identically to a GNU software product, ie programme and
   /* return pointer to array of pointers to rows */    software can be distributed freely for non commercial use. Latest version
   return m;    can be accessed at http://euroreves.ined.fr/imach .
 }  
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 /****************** free_imatrix *************************/    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 void free_imatrix(m,nrl,nrh,ncl,nch)    
       int **m;    **********************************************************************/
       long nch,ncl,nrh,nrl;  /*
      /* free an int matrix allocated by imatrix() */    main
 {    read parameterfile
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    read datafile
   free((FREE_ARG) (m+nrl-NR_END));    concatwav
 }    freqsummary
     if (mle >= 1)
 /******************* matrix *******************************/      mlikeli
 double **matrix(long nrl, long nrh, long ncl, long nch)    print results files
 {    if mle==1 
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;       computes hessian
   double **m;    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    open gnuplot file
   if (!m) nrerror("allocation failure 1 in matrix()");    open html file
   m += NR_END;    period (stable) prevalence
   m -= nrl;     for age prevalim()
     h Pij x
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    variance of p varprob
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    forecasting if prevfcast==1 prevforecast call prevalence()
   m[nrl] += NR_END;    health expectancies
   m[nrl] -= ncl;    Variance-covariance of DFLE
     prevalence()
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;     movingaverage()
   return m;    varevsij() 
 }    if popbased==1 varevsij(,popbased)
     total life expectancies
 /*************************free matrix ************************/    Variance of period (stable) prevalence
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)   end
 {  */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  
 }  
    
 /******************* ma3x *******************************/  #include <math.h>
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  #include <stdio.h>
 {  #include <stdlib.h>
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  #include <string.h>
   double ***m;  #include <unistd.h>
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #include <limits.h>
   if (!m) nrerror("allocation failure 1 in matrix()");  #include <sys/types.h>
   m += NR_END;  #include <sys/stat.h>
   m -= nrl;  #include <errno.h>
   extern int errno;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /* #include <sys/time.h> */
   m[nrl] += NR_END;  #include <time.h>
   m[nrl] -= ncl;  #include "timeval.h"
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /* #include <libintl.h> */
   /* #define _(String) gettext (String) */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  #define MAXLINE 256
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  #define GNUPLOTPROGRAM "gnuplot"
   for (j=ncl+1; j<=nch; j++)  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
     m[nrl][j]=m[nrl][j-1]+nlay;  #define FILENAMELENGTH 132
    
   for (i=nrl+1; i<=nrh; i++) {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
   }  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   return m;  
 }  #define NINTERVMAX 8
   #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 /*************************free ma3x ************************/  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define NCOVMAX 20 /* Maximum number of covariates */
 {  #define MAXN 20000
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define YEARM 12. /* Number of months per year */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define AGESUP 130
   free((FREE_ARG)(m+nrl-NR_END));  #define AGEBASE 40
 }  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   #ifdef UNIX
 /***************** f1dim *************************/  #define DIRSEPARATOR '/'
 extern int ncom;  #define CHARSEPARATOR "/"
 extern double *pcom,*xicom;  #define ODIRSEPARATOR '\\'
 extern double (*nrfunc)(double []);  #else
    #define DIRSEPARATOR '\\'
 double f1dim(double x)  #define CHARSEPARATOR "\\"
 {  #define ODIRSEPARATOR '/'
   int j;  #endif
   double f;  
   double *xt;  /* $Id$ */
    /* $State$ */
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  char version[]="Imach version 0.98k, June 2006, INED-EUROREVES-Institut de longevite ";
   f=(*nrfunc)(xt);  char fullversion[]="$Revision$ $Date$"; 
   free_vector(xt,1,ncom);  char strstart[80];
   return f;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 }  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   int nvar=0;
 /*****************brent *************************/  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int npar=NPARMAX;
 {  int nlstate=2; /* Number of live states */
   int iter;  int ndeath=1; /* Number of dead states */
   double a,b,d,etemp;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   double fu,fv,fw,fx;  int popbased=0;
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;  int *wav; /* Number of waves for this individuual 0 is possible */
   double e=0.0;  int maxwav=0; /* Maxim number of waves */
    int jmin=0, jmax=0; /* min, max spacing between 2 waves */
   a=(ax < cx ? ax : cx);  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   b=(ax > cx ? ax : cx);  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
   x=w=v=bx;                     to the likelihood and the sum of weights (done by funcone)*/
   fw=fv=fx=(*f)(x);  int mle=1, weightopt=0;
   for (iter=1;iter<=ITMAX;iter++) {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
     xm=0.5*(a+b);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     printf(".");fflush(stdout);  double jmean=1; /* Mean space between 2 waves */
 #ifdef DEBUG  double **oldm, **newm, **savm; /* Working pointers to matrices */
     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);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 #endif  FILE *ficlog, *ficrespow;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  int globpr=0; /* Global variable for printing or not */
       *xmin=x;  double fretone; /* Only one call to likelihood */
       return fx;  long ipmx=0; /* Number of contributions */
     }  double sw; /* Sum of weights */
     ftemp=fu;  char filerespow[FILENAMELENGTH];
     if (fabs(e) > tol1) {  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       r=(x-w)*(fx-fv);  FILE *ficresilk;
       q=(x-v)*(fx-fw);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       p=(x-v)*q-(x-w)*r;  FILE *ficresprobmorprev;
       q=2.0*(q-r);  FILE *fichtm, *fichtmcov; /* Html File */
       if (q > 0.0) p = -p;  FILE *ficreseij;
       q=fabs(q);  char filerese[FILENAMELENGTH];
       etemp=e;  FILE *ficresstdeij;
       e=d;  char fileresstde[FILENAMELENGTH];
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  FILE *ficrescveij;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  char filerescve[FILENAMELENGTH];
       else {  FILE  *ficresvij;
         d=p/q;  char fileresv[FILENAMELENGTH];
         u=x+d;  FILE  *ficresvpl;
         if (u-a < tol2 || b-u < tol2)  char fileresvpl[FILENAMELENGTH];
           d=SIGN(tol1,xm-x);  char title[MAXLINE];
       }  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     } else {  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     }  char command[FILENAMELENGTH];
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  int  outcmd=0;
     fu=(*f)(u);  
     if (fu <= fx) {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  char filelog[FILENAMELENGTH]; /* Log file */
         SHFT(fv,fw,fx,fu)  char filerest[FILENAMELENGTH];
         } else {  char fileregp[FILENAMELENGTH];
           if (u < x) a=u; else b=u;  char popfile[FILENAMELENGTH];
           if (fu <= fw || w == x) {  
             v=w;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
             w=u;  
             fv=fw;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
             fw=fu;  struct timezone tzp;
           } else if (fu <= fv || v == x || v == w) {  extern int gettimeofday();
             v=u;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
             fv=fu;  long time_value;
           }  extern long time();
         }  char strcurr[80], strfor[80];
   }  
   nrerror("Too many iterations in brent");  char *endptr;
   *xmin=x;  long lval;
   return fx;  double dval;
 }  
   #define NR_END 1
 /****************** mnbrak ***********************/  #define FREE_ARG char*
   #define FTOL 1.0e-10
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))  #define NRANSI 
 {  #define ITMAX 200 
   double ulim,u,r,q, dum;  
   double fu;  #define TOL 2.0e-4 
    
   *fa=(*func)(*ax);  #define CGOLD 0.3819660 
   *fb=(*func)(*bx);  #define ZEPS 1.0e-10 
   if (*fb > *fa) {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  #define GOLD 1.618034 
       }  #define GLIMIT 100.0 
   *cx=(*bx)+GOLD*(*bx-*ax);  #define TINY 1.0e-20 
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  static double maxarg1,maxarg2;
     r=(*bx-*ax)*(*fb-*fc);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     q=(*bx-*cx)*(*fb-*fa);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #define rint(a) floor(a+0.5)
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);  static double sqrarg;
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       fu=(*func)(u);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       if (fu < *fc) {  int agegomp= AGEGOMP;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  int imx; 
           }  int stepm=1;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  /* Stepm, step in month: minimum step interpolation*/
       u=ulim;  
       fu=(*func)(u);  int estepm;
     } else {  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);  int m,nb;
     }  long *num;
     SHFT(*ax,*bx,*cx,u)  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       SHFT(*fa,*fb,*fc,fu)  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       }  double **pmmij, ***probs;
 }  double *ageexmed,*agecens;
   double dateintmean=0;
 /*************** linmin ************************/  
   double *weight;
 int ncom;  int **s; /* Status */
 double *pcom,*xicom;  double *agedc, **covar, idx;
 double (*nrfunc)(double []);  int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
    double *lsurv, *lpop, *tpop;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double brent(double ax, double bx, double cx,  double ftolhess; /* Tolerance for computing hessian */
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);  /**************** split *************************/
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
               double *fc, double (*func)(double));  {
   int j;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   double xx,xmin,bx,ax;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   double fx,fb,fa;    */ 
      char  *ss;                            /* pointer */
   ncom=n;    int   l1, l2;                         /* length counters */
   pcom=vector(1,n);  
   xicom=vector(1,n);    l1 = strlen(path );                   /* length of path */
   nrfunc=func;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   for (j=1;j<=n;j++) {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     pcom[j]=p[j];    if ( ss == NULL ) {                   /* no directory, so determine current directory */
     xicom[j]=xi[j];      strcpy( name, path );               /* we got the fullname name because no directory */
   }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   ax=0.0;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   xx=1.0;      /* get current working directory */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      /*    extern  char* getcwd ( char *buf , int len);*/
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 #ifdef DEBUG        return( GLOCK_ERROR_GETCWD );
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      }
 #endif      /* got dirc from getcwd*/
   for (j=1;j<=n;j++) {      printf(" DIRC = %s \n",dirc);
     xi[j] *= xmin;    } else {                              /* strip direcotry from path */
     p[j] += xi[j];      ss++;                               /* after this, the filename */
   }      l2 = strlen( ss );                  /* length of filename */
   free_vector(xicom,1,n);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   free_vector(pcom,1,n);      strcpy( name, ss );         /* save file name */
 }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
 /*************** powell ************************/      printf(" DIRC2 = %s \n",dirc);
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    }
             double (*func)(double []))    /* We add a separator at the end of dirc if not exists */
 {    l1 = strlen( dirc );                  /* length of directory */
   void linmin(double p[], double xi[], int n, double *fret,    if( dirc[l1-1] != DIRSEPARATOR ){
               double (*func)(double []));      dirc[l1] =  DIRSEPARATOR;
   int i,ibig,j;      dirc[l1+1] = 0; 
   double del,t,*pt,*ptt,*xit;      printf(" DIRC3 = %s \n",dirc);
   double fp,fptt;    }
   double *xits;    ss = strrchr( name, '.' );            /* find last / */
   pt=vector(1,n);    if (ss >0){
   ptt=vector(1,n);      ss++;
   xit=vector(1,n);      strcpy(ext,ss);                     /* save extension */
   xits=vector(1,n);      l1= strlen( name);
   *fret=(*func)(p);      l2= strlen(ss)+1;
   for (j=1;j<=n;j++) pt[j]=p[j];      strncpy( finame, name, l1-l2);
   for (*iter=1;;++(*iter)) {      finame[l1-l2]= 0;
     fp=(*fret);    }
     ibig=0;  
     del=0.0;    return( 0 );                          /* we're done */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  }
     for (i=1;i<=n;i++)  
       printf(" %d %.12f",i, p[i]);  
     printf("\n");  /******************************************/
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  void replace_back_to_slash(char *s, char*t)
       fptt=(*fret);  {
 #ifdef DEBUG    int i;
       printf("fret=%lf \n",*fret);    int lg=0;
 #endif    i=0;
       printf("%d",i);fflush(stdout);    lg=strlen(t);
       linmin(p,xit,n,fret,func);    for(i=0; i<= lg; i++) {
       if (fabs(fptt-(*fret)) > del) {      (s[i] = t[i]);
         del=fabs(fptt-(*fret));      if (t[i]== '\\') s[i]='/';
         ibig=i;    }
       }  }
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));  int nbocc(char *s, char occ)
       for (j=1;j<=n;j++) {  {
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    int i,j=0;
         printf(" x(%d)=%.12e",j,xit[j]);    int lg=20;
       }    i=0;
       for(j=1;j<=n;j++)    lg=strlen(s);
         printf(" p=%.12e",p[j]);    for(i=0; i<= lg; i++) {
       printf("\n");    if  (s[i] == occ ) j++;
 #endif    }
     }    return j;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  }
 #ifdef DEBUG  
       int k[2],l;  void cutv(char *u,char *v, char*t, char occ)
       k[0]=1;  {
       k[1]=-1;    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       printf("Max: %.12e",(*func)(p));       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       for (j=1;j<=n;j++)       gives u="abcedf" and v="ghi2j" */
         printf(" %.12e",p[j]);    int i,lg,j,p=0;
       printf("\n");    i=0;
       for(l=0;l<=1;l++) {    for(j=0; j<=strlen(t)-1; j++) {
         for (j=1;j<=n;j++) {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
           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]);  
         }    lg=strlen(t);
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    for(j=0; j<p; j++) {
       }      (u[j] = t[j]);
 #endif    }
        u[p]='\0';
   
       free_vector(xit,1,n);     for(j=0; j<= lg; j++) {
       free_vector(xits,1,n);      if (j>=(p+1))(v[j-p-1] = t[j]);
       free_vector(ptt,1,n);    }
       free_vector(pt,1,n);  }
       return;  
     }  /********************** nrerror ********************/
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  
     for (j=1;j<=n;j++) {  void nrerror(char error_text[])
       ptt[j]=2.0*p[j]-pt[j];  {
       xit[j]=p[j]-pt[j];    fprintf(stderr,"ERREUR ...\n");
       pt[j]=p[j];    fprintf(stderr,"%s\n",error_text);
     }    exit(EXIT_FAILURE);
     fptt=(*func)(ptt);  }
     if (fptt < fp) {  /*********************** vector *******************/
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  double *vector(int nl, int nh)
       if (t < 0.0) {  {
         linmin(p,xit,n,fret,func);    double *v;
         for (j=1;j<=n;j++) {    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
           xi[j][ibig]=xi[j][n];    if (!v) nrerror("allocation failure in vector");
           xi[j][n]=xit[j];    return v-nl+NR_END;
         }  }
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  /************************ free vector ******************/
         for(j=1;j<=n;j++)  void free_vector(double*v, int nl, int nh)
           printf(" %.12e",xit[j]);  {
         printf("\n");    free((FREE_ARG)(v+nl-NR_END));
 #endif  }
       }  
     }  /************************ivector *******************************/
   }  int *ivector(long nl,long nh)
 }  {
     int *v;
 /**** Prevalence limit ****************/    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     if (!v) nrerror("allocation failure in ivector");
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    return v-nl+NR_END;
 {  }
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  
      matrix by transitions matrix until convergence is reached */  /******************free ivector **************************/
   void free_ivector(int *v, long nl, long nh)
   int i, ii,j,k;  {
   double min, max, maxmin, maxmax,sumnew=0.;    free((FREE_ARG)(v+nl-NR_END));
   double **matprod2();  }
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;  /************************lvector *******************************/
   double agefin, delaymax=50 ; /* Max number of years to converge */  long *lvector(long nl,long nh)
   {
   for (ii=1;ii<=nlstate+ndeath;ii++)    long *v;
     for (j=1;j<=nlstate+ndeath;j++){    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    if (!v) nrerror("allocation failure in ivector");
     }    return v-nl+NR_END;
   }
    cov[1]=1.;  
    /******************free lvector **************************/
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  void free_lvector(long *v, long nl, long nh)
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  {
     newm=savm;    free((FREE_ARG)(v+nl-NR_END));
     /* Covariates have to be included here again */  }
      cov[2]=agefin;  
    /******************* imatrix *******************************/
       for (k=1; k<=cptcovn;k++) {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
         /*      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]]);*/  { 
       }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    int **m; 
       for (k=1; k<=cptcovprod;k++)    
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    if (!m) nrerror("allocation failure 1 in matrix()"); 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    m += NR_END; 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    m -= nrl; 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    
     
     savm=oldm;    /* allocate rows and set pointers to them */ 
     oldm=newm;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     maxmax=0.;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     for(j=1;j<=nlstate;j++){    m[nrl] += NR_END; 
       min=1.;    m[nrl] -= ncl; 
       max=0.;    
       for(i=1; i<=nlstate; i++) {    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
         sumnew=0;    
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    /* return pointer to array of pointers to rows */ 
         prlim[i][j]= newm[i][j]/(1-sumnew);    return m; 
         max=FMAX(max,prlim[i][j]);  } 
         min=FMIN(min,prlim[i][j]);  
       }  /****************** free_imatrix *************************/
       maxmin=max-min;  void free_imatrix(m,nrl,nrh,ncl,nch)
       maxmax=FMAX(maxmax,maxmin);        int **m;
     }        long nch,ncl,nrh,nrl; 
     if(maxmax < ftolpl){       /* free an int matrix allocated by imatrix() */ 
       return prlim;  { 
     }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   }    free((FREE_ARG) (m+nrl-NR_END)); 
 }  } 
   
 /*************** transition probabilities ***************/  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  {
 {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   double s1, s2;    double **m;
   /*double t34;*/  
   int i,j,j1, nc, ii, jj;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
     for(i=1; i<= nlstate; i++){    m += NR_END;
     for(j=1; j<i;j++){    m -= nrl;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         /*s2 += param[i][j][nc]*cov[nc];*/    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    m[nrl] += NR_END;
       }    m[nrl] -= ncl;
       ps[i][j]=s2;  
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     }    return m;
     for(j=i+1; j<=nlstate+ndeath;j++){    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){     */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  }
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  
       }  /*************************free matrix ************************/
       ps[i][j]=s2;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     }  {
   }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     /*ps[3][2]=1;*/    free((FREE_ARG)(m+nrl-NR_END));
   }
   for(i=1; i<= nlstate; i++){  
      s1=0;  /******************* ma3x *******************************/
     for(j=1; j<i; j++)  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       s1+=exp(ps[i][j]);  {
     for(j=i+1; j<=nlstate+ndeath; j++)    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       s1+=exp(ps[i][j]);    double ***m;
     ps[i][i]=1./(s1+1.);  
     for(j=1; j<i; j++)    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       ps[i][j]= exp(ps[i][j])*ps[i][i];    if (!m) nrerror("allocation failure 1 in matrix()");
     for(j=i+1; j<=nlstate+ndeath; j++)    m += NR_END;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    m -= nrl;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  
   } /* end i */    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    m[nrl] += NR_END;
     for(jj=1; jj<= nlstate+ndeath; jj++){    m[nrl] -= ncl;
       ps[ii][jj]=0;  
       ps[ii][ii]=1;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     }  
   }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     m[nrl][ncl] += NR_END;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    m[nrl][ncl] -= nll;
     for(jj=1; jj<= nlstate+ndeath; jj++){    for (j=ncl+1; j<=nch; j++) 
      printf("%lf ",ps[ii][jj]);      m[nrl][j]=m[nrl][j-1]+nlay;
    }    
     printf("\n ");    for (i=nrl+1; i<=nrh; i++) {
     }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     printf("\n ");printf("%lf ",cov[2]);*/      for (j=ncl+1; j<=nch; j++) 
 /*        m[i][j]=m[i][j-1]+nlay;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    }
   goto end;*/    return m; 
     return ps;    /*  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)
     */
 /**************** Product of 2 matrices ******************/  }
   
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  /*************************free ma3x ************************/
 {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  {
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   /* in, b, out are matrice of pointers which should have been initialized    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      before: only the contents of out is modified. The function returns    free((FREE_ARG)(m+nrl-NR_END));
      a pointer to pointers identical to out */  }
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)  /*************** function subdirf ***********/
     for(k=ncolol; k<=ncoloh; k++)  char *subdirf(char fileres[])
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  {
         out[i][k] +=in[i][j]*b[j][k];    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
   return out;    strcat(tmpout,"/"); /* Add to the right */
 }    strcat(tmpout,fileres);
     return tmpout;
   }
 /************* Higher Matrix Product ***************/  
   /*************** function subdirf2 ***********/
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  char *subdirf2(char fileres[], char *preop)
 {  {
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    
      duration (i.e. until    /* Caution optionfilefiname is hidden */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    strcpy(tmpout,optionfilefiname);
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    strcat(tmpout,"/");
      (typically every 2 years instead of every month which is too big).    strcat(tmpout,preop);
      Model is determined by parameters x and covariates have to be    strcat(tmpout,fileres);
      included manually here.    return tmpout;
   }
      */  
   /*************** function subdirf3 ***********/
   int i, j, d, h, k;  char *subdirf3(char fileres[], char *preop, char *preop2)
   double **out, cov[NCOVMAX];  {
   double **newm;    
     /* Caution optionfilefiname is hidden */
   /* Hstepm could be zero and should return the unit matrix */    strcpy(tmpout,optionfilefiname);
   for (i=1;i<=nlstate+ndeath;i++)    strcat(tmpout,"/");
     for (j=1;j<=nlstate+ndeath;j++){    strcat(tmpout,preop);
       oldm[i][j]=(i==j ? 1.0 : 0.0);    strcat(tmpout,preop2);
       po[i][j][0]=(i==j ? 1.0 : 0.0);    strcat(tmpout,fileres);
     }    return tmpout;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  }
   for(h=1; h <=nhstepm; h++){  
     for(d=1; d <=hstepm; d++){  /***************** f1dim *************************/
       newm=savm;  extern int ncom; 
       /* Covariates have to be included here again */  extern double *pcom,*xicom;
       cov[1]=1.;  extern double (*nrfunc)(double []); 
       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]]];  double f1dim(double x) 
       for (k=1; k<=cptcovage;k++)  { 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    int j; 
       for (k=1; k<=cptcovprod;k++)    double f;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    double *xt; 
    
     xt=vector(1,ncom); 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    f=(*nrfunc)(xt); 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    free_vector(xt,1,ncom); 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    return f; 
       savm=oldm;  } 
       oldm=newm;  
     }  /*****************brent *************************/
     for(i=1; i<=nlstate+ndeath; i++)  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       for(j=1;j<=nlstate+ndeath;j++) {  { 
         po[i][j][h]=newm[i][j];    int iter; 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    double a,b,d,etemp;
          */    double fu,fv,fw,fx;
       }    double ftemp;
   } /* end h */    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   return po;    double e=0.0; 
 }   
     a=(ax < cx ? ax : cx); 
     b=(ax > cx ? ax : cx); 
 /*************** log-likelihood *************/    x=w=v=bx; 
 double func( double *x)    fw=fv=fx=(*f)(x); 
 {    for (iter=1;iter<=ITMAX;iter++) { 
   int i, ii, j, k, mi, d, kk;      xm=0.5*(a+b); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   double **out;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   double sw; /* Sum of weights */      printf(".");fflush(stdout);
   double lli; /* Individual log likelihood */      fprintf(ficlog,".");fflush(ficlog);
   long ipmx;  #ifdef DEBUG
   /*extern weight */      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);
   /* We are differentiating ll according to initial status */      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   /*for(i=1;i<imx;i++)  #endif
     printf(" %d\n",s[4][i]);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   */        *xmin=x; 
   cov[1]=1.;        return fx; 
       } 
   for(k=1; k<=nlstate; k++) ll[k]=0.;      ftemp=fu;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      if (fabs(e) > tol1) { 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        r=(x-w)*(fx-fv); 
     for(mi=1; mi<= wav[i]-1; mi++){        q=(x-v)*(fx-fw); 
       for (ii=1;ii<=nlstate+ndeath;ii++)        p=(x-v)*q-(x-w)*r; 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        q=2.0*(q-r); 
       for(d=0; d<dh[mi][i]; d++){        if (q > 0.0) p = -p; 
         newm=savm;        q=fabs(q); 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        etemp=e; 
         for (kk=1; kk<=cptcovage;kk++) {        e=d; 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        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)); 
                else { 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          d=p/q; 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));          u=x+d; 
         savm=oldm;          if (u-a < tol2 || b-u < tol2) 
         oldm=newm;            d=SIGN(tol1,xm-x); 
                } 
              } else { 
       } /* end mult */        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
            } 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      fu=(*f)(u); 
       ipmx +=1;      if (fu <= fx) { 
       sw += weight[i];        if (u >= x) a=x; else b=x; 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        SHFT(v,w,x,u) 
     } /* end of wave */          SHFT(fv,fw,fx,fu) 
   } /* end of individual */          } else { 
             if (u < x) a=u; else b=u; 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];            if (fu <= fw || w == x) { 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */              v=w; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */              w=u; 
   return -l;              fv=fw; 
 }              fw=fu; 
             } else if (fu <= fv || v == x || v == w) { 
               v=u; 
 /*********** Maximum Likelihood Estimation ***************/              fv=fu; 
             } 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))          } 
 {    } 
   int i,j, iter;    nrerror("Too many iterations in brent"); 
   double **xi,*delti;    *xmin=x; 
   double fret;    return fx; 
   xi=matrix(1,npar,1,npar);  } 
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)  /****************** mnbrak ***********************/
       xi[i][j]=(i==j ? 1.0 : 0.0);  
   printf("Powell\n");  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   powell(p,xi,npar,ftol,&iter,&fret,func);              double (*func)(double)) 
   { 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    double ulim,u,r,q, dum;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    double fu; 
    
 }    *fa=(*func)(*ax); 
     *fb=(*func)(*bx); 
 /**** Computes Hessian and covariance matrix ***/    if (*fb > *fa) { 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      SHFT(dum,*ax,*bx,dum) 
 {        SHFT(dum,*fb,*fa,dum) 
   double  **a,**y,*x,pd;        } 
   double **hess;    *cx=(*bx)+GOLD*(*bx-*ax); 
   int i, j,jk;    *fc=(*func)(*cx); 
   int *indx;    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
   double hessii(double p[], double delta, int theta, double delti[]);      q=(*bx-*cx)*(*fb-*fa); 
   double hessij(double p[], double delti[], int i, int j);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   void lubksb(double **a, int npar, int *indx, double b[]) ;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   void ludcmp(double **a, int npar, int *indx, double *d) ;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if ((*bx-u)*(u-*cx) > 0.0) { 
   hess=matrix(1,npar,1,npar);        fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
   printf("\nCalculation of the hessian matrix. Wait...\n");        fu=(*func)(u); 
   for (i=1;i<=npar;i++){        if (fu < *fc) { 
     printf("%d",i);fflush(stdout);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     hess[i][i]=hessii(p,ftolhess,i,delti);            SHFT(*fb,*fc,fu,(*func)(u)) 
     /*printf(" %f ",p[i]);*/            } 
     /*printf(" %lf ",hess[i][i]);*/      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   }        u=ulim; 
          fu=(*func)(u); 
   for (i=1;i<=npar;i++) {      } else { 
     for (j=1;j<=npar;j++)  {        u=(*cx)+GOLD*(*cx-*bx); 
       if (j>i) {        fu=(*func)(u); 
         printf(".%d%d",i,j);fflush(stdout);      } 
         hess[i][j]=hessij(p,delti,i,j);      SHFT(*ax,*bx,*cx,u) 
         hess[j][i]=hess[i][j];            SHFT(*fa,*fb,*fc,fu) 
         /*printf(" %lf ",hess[i][j]);*/        } 
       }  } 
     }  
   }  /*************** linmin ************************/
   printf("\n");  
   int ncom; 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  double *pcom,*xicom;
    double (*nrfunc)(double []); 
   a=matrix(1,npar,1,npar);   
   y=matrix(1,npar,1,npar);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   x=vector(1,npar);  { 
   indx=ivector(1,npar);    double brent(double ax, double bx, double cx, 
   for (i=1;i<=npar;i++)                 double (*f)(double), double tol, double *xmin); 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    double f1dim(double x); 
   ludcmp(a,npar,indx,&pd);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
   for (j=1;j<=npar;j++) {    int j; 
     for (i=1;i<=npar;i++) x[i]=0;    double xx,xmin,bx,ax; 
     x[j]=1;    double fx,fb,fa;
     lubksb(a,npar,indx,x);   
     for (i=1;i<=npar;i++){    ncom=n; 
       matcov[i][j]=x[i];    pcom=vector(1,n); 
     }    xicom=vector(1,n); 
   }    nrfunc=func; 
     for (j=1;j<=n;j++) { 
   printf("\n#Hessian matrix#\n");      pcom[j]=p[j]; 
   for (i=1;i<=npar;i++) {      xicom[j]=xi[j]; 
     for (j=1;j<=npar;j++) {    } 
       printf("%.3e ",hess[i][j]);    ax=0.0; 
     }    xx=1.0; 
     printf("\n");    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   }    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   #ifdef DEBUG
   /* Recompute Inverse */    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   for (i=1;i<=npar;i++)    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  #endif
   ludcmp(a,npar,indx,&pd);    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
   /*  printf("\n#Hessian matrix recomputed#\n");      p[j] += xi[j]; 
     } 
   for (j=1;j<=npar;j++) {    free_vector(xicom,1,n); 
     for (i=1;i<=npar;i++) x[i]=0;    free_vector(pcom,1,n); 
     x[j]=1;  } 
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){  char *asc_diff_time(long time_sec, char ascdiff[])
       y[i][j]=x[i];  {
       printf("%.3e ",y[i][j]);    long sec_left, days, hours, minutes;
     }    days = (time_sec) / (60*60*24);
     printf("\n");    sec_left = (time_sec) % (60*60*24);
   }    hours = (sec_left) / (60*60) ;
   */    sec_left = (sec_left) %(60*60);
     minutes = (sec_left) /60;
   free_matrix(a,1,npar,1,npar);    sec_left = (sec_left) % (60);
   free_matrix(y,1,npar,1,npar);    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   free_vector(x,1,npar);    return ascdiff;
   free_ivector(indx,1,npar);  }
   free_matrix(hess,1,npar,1,npar);  
   /*************** powell ************************/
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 }              double (*func)(double [])) 
   { 
 /*************** hessian matrix ****************/    void linmin(double p[], double xi[], int n, double *fret, 
 double hessii( double x[], double delta, int theta, double delti[])                double (*func)(double [])); 
 {    int i,ibig,j; 
   int i;    double del,t,*pt,*ptt,*xit;
   int l=1, lmax=20;    double fp,fptt;
   double k1,k2;    double *xits;
   double p2[NPARMAX+1];    int niterf, itmp;
   double res;  
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    pt=vector(1,n); 
   double fx;    ptt=vector(1,n); 
   int k=0,kmax=10;    xit=vector(1,n); 
   double l1;    xits=vector(1,n); 
     *fret=(*func)(p); 
   fx=func(x);    for (j=1;j<=n;j++) pt[j]=p[j]; 
   for (i=1;i<=npar;i++) p2[i]=x[i];    for (*iter=1;;++(*iter)) { 
   for(l=0 ; l <=lmax; l++){      fp=(*fret); 
     l1=pow(10,l);      ibig=0; 
     delts=delt;      del=0.0; 
     for(k=1 ; k <kmax; k=k+1){      last_time=curr_time;
       delt = delta*(l1*k);      (void) gettimeofday(&curr_time,&tzp);
       p2[theta]=x[theta] +delt;      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);
       k1=func(p2)-fx;      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); fflush(ficlog);
       p2[theta]=x[theta]-delt;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
       k2=func(p2)-fx;     for (i=1;i<=n;i++) {
       /*res= (k1-2.0*fx+k2)/delt/delt; */        printf(" %d %.12f",i, p[i]);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        fprintf(ficlog," %d %.12lf",i, p[i]);
              fprintf(ficrespow," %.12lf", p[i]);
 #ifdef DEBUG      }
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);      printf("\n");
 #endif      fprintf(ficlog,"\n");
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      fprintf(ficrespow,"\n");fflush(ficrespow);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      if(*iter <=3){
         k=kmax;        tm = *localtime(&curr_time.tv_sec);
       }        strcpy(strcurr,asctime(&tm));
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  /*       asctime_r(&tm,strcurr); */
         k=kmax; l=lmax*10.;        forecast_time=curr_time; 
       }        itmp = strlen(strcurr);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         delts=delt;          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);
     }        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){
   delti[theta]=delts;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   return res;          tmf = *localtime(&forecast_time.tv_sec);
    /*      asctime_r(&tmf,strfor); */
 }          strcpy(strfor,asctime(&tmf));
           itmp = strlen(strfor);
 double hessij( double x[], double delti[], int thetai,int thetaj)          if(strfor[itmp-1]=='\n')
 {          strfor[itmp-1]='\0';
   int i;          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);
   int l=1, l1, lmax=20;          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);
   double k1,k2,k3,k4,res,fx;        }
   double p2[NPARMAX+1];      }
   int k;      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   fx=func(x);        fptt=(*fret); 
   for (k=1; k<=2; k++) {  #ifdef DEBUG
     for (i=1;i<=npar;i++) p2[i]=x[i];        printf("fret=%lf \n",*fret);
     p2[thetai]=x[thetai]+delti[thetai]/k;        fprintf(ficlog,"fret=%lf \n",*fret);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  #endif
     k1=func(p2)-fx;        printf("%d",i);fflush(stdout);
          fprintf(ficlog,"%d",i);fflush(ficlog);
     p2[thetai]=x[thetai]+delti[thetai]/k;        linmin(p,xit,n,fret,func); 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        if (fabs(fptt-(*fret)) > del) { 
     k2=func(p2)-fx;          del=fabs(fptt-(*fret)); 
            ibig=i; 
     p2[thetai]=x[thetai]-delti[thetai]/k;        } 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  #ifdef DEBUG
     k3=func(p2)-fx;        printf("%d %.12e",i,(*fret));
          fprintf(ficlog,"%d %.12e",i,(*fret));
     p2[thetai]=x[thetai]-delti[thetai]/k;        for (j=1;j<=n;j++) {
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     k4=func(p2)-fx;          printf(" x(%d)=%.12e",j,xit[j]);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
 #ifdef DEBUG        }
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        for(j=1;j<=n;j++) {
 #endif          printf(" p=%.12e",p[j]);
   }          fprintf(ficlog," p=%.12e",p[j]);
   return res;        }
 }        printf("\n");
         fprintf(ficlog,"\n");
 /************** Inverse of matrix **************/  #endif
 void ludcmp(double **a, int n, int *indx, double *d)      } 
 {      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   int i,imax,j,k;  #ifdef DEBUG
   double big,dum,sum,temp;        int k[2],l;
   double *vv;        k[0]=1;
          k[1]=-1;
   vv=vector(1,n);        printf("Max: %.12e",(*func)(p));
   *d=1.0;        fprintf(ficlog,"Max: %.12e",(*func)(p));
   for (i=1;i<=n;i++) {        for (j=1;j<=n;j++) {
     big=0.0;          printf(" %.12e",p[j]);
     for (j=1;j<=n;j++)          fprintf(ficlog," %.12e",p[j]);
       if ((temp=fabs(a[i][j])) > big) big=temp;        }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        printf("\n");
     vv[i]=1.0/big;        fprintf(ficlog,"\n");
   }        for(l=0;l<=1;l++) {
   for (j=1;j<=n;j++) {          for (j=1;j<=n;j++) {
     for (i=1;i<j;i++) {            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       sum=a[i][j];            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       a[i][j]=sum;          }
     }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     big=0.0;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for (i=j;i<=n;i++) {        }
       sum=a[i][j];  #endif
       for (k=1;k<j;k++)  
         sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;        free_vector(xit,1,n); 
       if ( (dum=vv[i]*fabs(sum)) >= big) {        free_vector(xits,1,n); 
         big=dum;        free_vector(ptt,1,n); 
         imax=i;        free_vector(pt,1,n); 
       }        return; 
     }      } 
     if (j != imax) {      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (k=1;k<=n;k++) {      for (j=1;j<=n;j++) { 
         dum=a[imax][k];        ptt[j]=2.0*p[j]-pt[j]; 
         a[imax][k]=a[j][k];        xit[j]=p[j]-pt[j]; 
         a[j][k]=dum;        pt[j]=p[j]; 
       }      } 
       *d = -(*d);      fptt=(*func)(ptt); 
       vv[imax]=vv[j];      if (fptt < fp) { 
     }        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     indx[j]=imax;        if (t < 0.0) { 
     if (a[j][j] == 0.0) a[j][j]=TINY;          linmin(p,xit,n,fret,func); 
     if (j != n) {          for (j=1;j<=n;j++) { 
       dum=1.0/(a[j][j]);            xi[j][ibig]=xi[j][n]; 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;            xi[j][n]=xit[j]; 
     }          }
   }  #ifdef DEBUG
   free_vector(vv,1,n);  /* Doesn't work */          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 ;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 }          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
 void lubksb(double **a, int n, int *indx, double b[])            fprintf(ficlog," %.12e",xit[j]);
 {          }
   int i,ii=0,ip,j;          printf("\n");
   double sum;          fprintf(ficlog,"\n");
    #endif
   for (i=1;i<=n;i++) {        }
     ip=indx[i];      } 
     sum=b[ip];    } 
     b[ip]=b[i];  } 
     if (ii)  
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  /**** Prevalence limit (stable or period prevalence)  ****************/
     else if (sum) ii=i;  
     b[i]=sum;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   }  {
   for (i=n;i>=1;i--) {    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     sum=b[i];       matrix by transitions matrix until convergence is reached */
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  
     b[i]=sum/a[i][i];    int i, ii,j,k;
   }    double min, max, maxmin, maxmax,sumnew=0.;
 }    double **matprod2();
     double **out, cov[NCOVMAX+1], **pmij();
 /************ Frequencies ********************/    double **newm;
 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)    double agefin, delaymax=50 ; /* Max number of years to converge */
 {  /* Some frequencies */  
      for (ii=1;ii<=nlstate+ndeath;ii++)
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;      for (j=1;j<=nlstate+ndeath;j++){
   double ***freq; /* Frequencies */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double *pp;      }
   double pos, k2, dateintsum=0,k2cpt=0;  
   FILE *ficresp;     cov[1]=1.;
   char fileresp[FILENAMELENGTH];   
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   pp=vector(1,nlstate);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      newm=savm;
   strcpy(fileresp,"p");      /* Covariates have to be included here again */
   strcat(fileresp,fileres);       cov[2]=agefin;
   if((ficresp=fopen(fileresp,"w"))==NULL) {    
     printf("Problem with prevalence resultfile: %s\n", fileresp);        for (k=1; k<=cptcovn;k++) {
     exit(0);          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]]);*/
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        }
   j1=0;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
          for (k=1; k<=cptcovprod;k++)
   j=cptcoveff;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
          /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   for(k1=1; k1<=j;k1++){        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     for(i1=1; i1<=ncodemax[k1];i1++){        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       j1++;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  
         scanf("%d", i);*/      savm=oldm;
       for (i=-1; i<=nlstate+ndeath; i++)        oldm=newm;
         for (jk=-1; jk<=nlstate+ndeath; jk++)        maxmax=0.;
           for(m=agemin; m <= agemax+3; m++)      for(j=1;j<=nlstate;j++){
             freq[i][jk][m]=0;        min=1.;
              max=0.;
       dateintsum=0;        for(i=1; i<=nlstate; i++) {
       k2cpt=0;          sumnew=0;
       for (i=1; i<=imx; i++) {          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         bool=1;          prlim[i][j]= newm[i][j]/(1-sumnew);
         if  (cptcovn>0) {          max=FMAX(max,prlim[i][j]);
           for (z1=1; z1<=cptcoveff; z1++)          min=FMIN(min,prlim[i][j]);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        }
               bool=0;        maxmin=max-min;
         }        maxmax=FMAX(maxmax,maxmin);
         if (bool==1) {      }
           for(m=firstpass; m<=lastpass; m++){      if(maxmax < ftolpl){
             k2=anint[m][i]+(mint[m][i]/12.);        return prlim;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      }
               if(agev[m][i]==0) agev[m][i]=agemax+1;    }
               if(agev[m][i]==1) agev[m][i]=agemax+2;  }
               if (m<lastpass) {  
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  /*************** transition probabilities ***************/ 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  
               }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
                {
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {    double s1, s2;
                 dateintsum=dateintsum+k2;    /*double t34;*/
                 k2cpt++;    int i,j,j1, nc, ii, jj;
               }  
             }      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];*/
                    s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
           }
       if  (cptcovn>0) {          ps[i][j]=s2;
         fprintf(ficresp, "\n#********** Variable ");  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        }
         fprintf(ficresp, "**********\n#");        for(j=i+1; j<=nlstate+ndeath;j++){
       }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       for(i=1; i<=nlstate;i++)            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
       fprintf(ficresp, "\n");          }
                ps[i][j]=s2;
       for(i=(int)agemin; i <= (int)agemax+3; i++){        }
         if(i==(int)agemax+3)      }
           printf("Total");      /*ps[3][2]=1;*/
         else      
           printf("Age %d", i);      for(i=1; i<= nlstate; i++){
         for(jk=1; jk <=nlstate ; jk++){        s1=0;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        for(j=1; j<i; j++){
             pp[jk] += freq[jk][m][i];          s1+=exp(ps[i][j]);
         }          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         for(jk=1; jk <=nlstate ; jk++){        }
           for(m=-1, pos=0; m <=0 ; m++)        for(j=i+1; j<=nlstate+ndeath; j++){
             pos += freq[jk][m][i];          s1+=exp(ps[i][j]);
           if(pp[jk]>=1.e-10)          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        }
           else        ps[i][i]=1./(s1+1.);
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        for(j=1; j<i; j++)
         }          ps[i][j]= exp(ps[i][j])*ps[i][i];
         for(j=i+1; j<=nlstate+ndeath; j++)
         for(jk=1; jk <=nlstate ; jk++){          ps[i][j]= exp(ps[i][j])*ps[i][i];
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
             pp[jk] += freq[jk][m][i];      } /* end i */
         }      
       for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         for(jk=1,pos=0; jk <=nlstate ; jk++)        for(jj=1; jj<= nlstate+ndeath; jj++){
           pos += pp[jk];          ps[ii][jj]=0;
         for(jk=1; jk <=nlstate ; jk++){          ps[ii][ii]=1;
           if(pos>=1.e-5)        }
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      }
           else      
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  
           if( i <= (int) agemax){  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
             if(pos>=1.e-5){  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  /*         printf("ddd %lf ",ps[ii][jj]); */
               probs[i][jk][j1]= pp[jk]/pos;  /*       } */
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  /*       printf("\n "); */
             }  /*        } */
             else  /*        printf("\n ");printf("%lf ",cov[2]); */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);         /*
           }        for(i=1; i<= npar; i++) printf("%f ",x[i]);
         }        goto end;*/
              return ps;
         for(jk=-1; jk <=nlstate+ndeath; jk++)  }
           for(m=-1; m <=nlstate+ndeath; m++)  
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  /**************** Product of 2 matrices ******************/
         if(i <= (int) agemax)  
           fprintf(ficresp,"\n");  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
         printf("\n");  {
       }    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     }       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   }    /* in, b, out are matrice of pointers which should have been initialized 
   dateintmean=dateintsum/k2cpt;       before: only the contents of out is modified. The function returns
         a pointer to pointers identical to out */
   fclose(ficresp);    long i, j, k;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    for(i=nrl; i<= nrh; i++)
   free_vector(pp,1,nlstate);      for(k=ncolol; k<=ncoloh; k++)
          for(j=ncl,out[i][k]=0.; j<=nch; j++)
   /* End of Freq */          out[i][k] +=in[i][j]*b[j][k];
 }  
     return out;
 /************ Prevalence ********************/  }
 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 */  
    /************* Higher Matrix Product ***************/
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   double *pp;  {
   double pos, k2;    /* Computes the transition matrix starting at age 'age' over 
        'nhstepm*hstepm*stepm' months (i.e. until
   pp=vector(1,nlstate);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);       nhstepm*hstepm matrices. 
         Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);       (typically every 2 years instead of every month which is too big 
   j1=0;       for the memory).
         Model is determined by parameters x and covariates have to be 
   j=cptcoveff;       included manually here. 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
         */
  for(k1=1; k1<=j;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){    int i, j, d, h, k;
       j1++;    double **out, cov[NCOVMAX+1];
      double **newm;
       for (i=-1; i<=nlstate+ndeath; i++)    
         for (jk=-1; jk<=nlstate+ndeath; jk++)      /* Hstepm could be zero and should return the unit matrix */
           for(m=agemin; m <= agemax+3; m++)    for (i=1;i<=nlstate+ndeath;i++)
             freq[i][jk][m]=0;      for (j=1;j<=nlstate+ndeath;j++){
              oldm[i][j]=(i==j ? 1.0 : 0.0);
       for (i=1; i<=imx; i++) {        po[i][j][0]=(i==j ? 1.0 : 0.0);
         bool=1;      }
         if  (cptcovn>0) {    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
           for (z1=1; z1<=cptcoveff; z1++)    for(h=1; h <=nhstepm; h++){
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      for(d=1; d <=hstepm; d++){
               bool=0;        newm=savm;
         }        /* Covariates have to be included here again */
         if (bool==1) {        cov[1]=1.;
           for(m=firstpass; m<=lastpass; m++){        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
             k2=anint[m][i]+(mint[m][i]/12.);        for (k=1; k<=cptcovn;k++) 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
               if(agev[m][i]==0) agev[m][i]=agemax+1;        for (k=1; k<=cptcovage;k++)
               if(agev[m][i]==1) agev[m][i]=agemax+2;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        for (k=1; k<=cptcovprod;k++)
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
             }  
           }  
         }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         for(i=(int)agemin; i <= (int)agemax+3; i++){        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
           for(jk=1; jk <=nlstate ; jk++){                     pmij(pmmij,cov,ncovmodel,x,nlstate));
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        savm=oldm;
               pp[jk] += freq[jk][m][i];        oldm=newm;
           }      }
           for(jk=1; jk <=nlstate ; jk++){      for(i=1; i<=nlstate+ndeath; i++)
             for(m=-1, pos=0; m <=0 ; m++)        for(j=1;j<=nlstate+ndeath;j++) {
             pos += freq[jk][m][i];          po[i][j][h]=newm[i][j];
         }          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
                }
          for(jk=1; jk <=nlstate ; jk++){      /*printf("h=%d ",h);*/
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    } /* end h */
              pp[jk] += freq[jk][m][i];  /*     printf("\n H=%d \n",h); */
          }    return po;
            }
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  
   
          for(jk=1; jk <=nlstate ; jk++){            /*************** log-likelihood *************/
            if( i <= (int) agemax){  double func( double *x)
              if(pos>=1.e-5){  {
                probs[i][jk][j1]= pp[jk]/pos;    int i, ii, j, k, mi, d, kk;
              }    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
            }    double **out;
          }    double sw; /* Sum of weights */
              double lli; /* Individual log likelihood */
         }    int s1, s2;
     }    double bbh, survp;
   }    long ipmx;
      /*extern weight */
      /* We are differentiating ll according to initial status */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   free_vector(pp,1,nlstate);    /*for(i=1;i<imx;i++) 
        printf(" %d\n",s[4][i]);
 }  /* End of Freq */    */
     cov[1]=1.;
 /************* Waves Concatenation ***************/  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  
 {    if(mle==1){
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      Death is a valid wave (if date is known).        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        for(mi=1; mi<= wav[i]-1; mi++){
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          for (ii=1;ii<=nlstate+ndeath;ii++)
      and mw[mi+1][i]. dh depends on stepm.            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);
   int i, mi, m;            }
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          for(d=0; d<dh[mi][i]; d++){
      double sum=0., jmean=0.;*/            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int j, k=0,jk, ju, jl;            for (kk=1; kk<=cptcovage;kk++) {
   double sum=0.;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   jmin=1e+5;            }
   jmax=-1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   jmean=0.;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for(i=1; i<=imx; i++){            savm=oldm;
     mi=0;            oldm=newm;
     m=firstpass;          } /* end mult */
     while(s[m][i] <= nlstate){        
       if(s[m][i]>=1)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         mw[++mi][i]=m;          /* But now since version 0.9 we anticipate for bias at large stepm.
       if(m >=lastpass)           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         break;           * (in months) between two waves is not a multiple of stepm, we rounded to 
       else           * the nearest (and in case of equal distance, to the lowest) interval but now
         m++;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     }/* end while */           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
     if (s[m][i] > nlstate){           * probability in order to take into account the bias as a fraction of the way
       mi++;     /* Death is another wave */           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
       /* if(mi==0)  never been interviewed correctly before death */           * -stepm/2 to stepm/2 .
          /* Only death is a correct wave */           * For stepm=1 the results are the same as for previous versions of Imach.
       mw[mi][i]=m;           * For stepm > 1 the results are less biased than in previous versions. 
     }           */
           s1=s[mw[mi][i]][i];
     wav[i]=mi;          s2=s[mw[mi+1][i]][i];
     if(mi==0)          bbh=(double)bh[mi][i]/(double)stepm; 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          /* bias bh is positive if real duration
   }           * is higher than the multiple of stepm and negative otherwise.
            */
   for(i=1; i<=imx; i++){          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     for(mi=1; mi<wav[i];mi++){          if( s2 > nlstate){ 
       if (stepm <=0)            /* i.e. if s2 is a death state and if the date of death is known 
         dh[mi][i]=1;               then the contribution to the likelihood is the probability to 
       else{               die between last step unit time and current  step unit time, 
         if (s[mw[mi+1][i]][i] > nlstate) {               which is also equal to probability to die before dh 
           if (agedc[i] < 2*AGESUP) {               minus probability to die before dh-stepm . 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);               In version up to 0.92 likelihood was computed
           if(j==0) j=1;  /* Survives at least one month after exam */          as if date of death was unknown. Death was treated as any other
           k=k+1;          health state: the date of the interview describes the actual state
           if (j >= jmax) jmax=j;          and not the date of a change in health state. The former idea was
           if (j <= jmin) jmin=j;          to consider that at each interview the state was recorded
           sum=sum+j;          (healthy, disable or death) and IMaCh was corrected; but when we
           /*if (j<0) printf("j=%d num=%d \n",j,i); */          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
         else{          stepm. It is no more the probability to die between last interview
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          and month of death but the probability to survive from last
           k=k+1;          interview up to one month before death multiplied by the
           if (j >= jmax) jmax=j;          probability to die within a month. Thanks to Chris
           else if (j <= jmin)jmin=j;          Jackson for correcting this bug.  Former versions increased
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          mortality artificially. The bad side is that we add another loop
           sum=sum+j;          which slows down the processing. The difference can be up to 10%
         }          lower mortality.
         jk= j/stepm;            */
         jl= j -jk*stepm;            lli=log(out[s1][s2] - savm[s1][s2]);
         ju= j -(jk+1)*stepm;  
         if(jl <= -ju)  
           dh[mi][i]=jk;          } else if  (s2==-2) {
         else            for (j=1,survp=0. ; j<=nlstate; j++) 
           dh[mi][i]=jk+1;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         if(dh[mi][i]==0)            /*survp += out[s1][j]; */
           dh[mi][i]=1; /* At least one step */            lli= log(survp);
       }          }
     }          
   }          else if  (s2==-4) { 
   jmean=sum/k;            for (j=3,survp=0. ; j<=nlstate; j++)  
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
  }            lli= log(survp); 
 /*********** Tricode ****************************/          } 
 void tricode(int *Tvar, int **nbcode, int imx)  
 {          else if  (s2==-5) { 
   int Ndum[20],ij=1, k, j, i;            for (j=1,survp=0. ; j<=2; j++)  
   int cptcode=0;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   cptcoveff=0;            lli= log(survp); 
            } 
   for (k=0; k<19; k++) Ndum[k]=0;          
   for (k=1; k<=7; k++) ncodemax[k]=0;          else{
             lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   for (j=1; j<=(cptcovn+2*cptcovprod); 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 */
     for (i=1; i<=imx; i++) {          } 
       ij=(int)(covar[Tvar[j]][i]);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       Ndum[ij]++;          /*if(lli ==000.0)*/
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          /*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 (ij > cptcode) cptcode=ij;          ipmx +=1;
     }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (i=0; i<=cptcode; i++) {        } /* end of wave */
       if(Ndum[i]!=0) ncodemax[j]++;      } /* end of individual */
     }    }  else if(mle==2){
     ij=1;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
     for (i=1; i<=ncodemax[j]; i++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
       for (k=0; k<=19; k++) {            for (j=1;j<=nlstate+ndeath;j++){
         if (Ndum[k] != 0) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           nbcode[Tvar[j]][ij]=k;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/            }
           ij++;          for(d=0; d<=dh[mi][i]; d++){
         }            newm=savm;
         if (ij > ncodemax[j]) break;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }              for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }              }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
  for (k=0; k<19; k++) Ndum[k]=0;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
  for (i=1; i<=ncovmodel-2; i++) {            oldm=newm;
       ij=Tvar[i];          } /* end mult */
       Ndum[ij]++;        
     }          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
  ij=1;          bbh=(double)bh[mi][i]/(double)stepm; 
  for (i=1; i<=10; i++) {          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
    if((Ndum[i]!=0) && (i<=ncovcol)){          ipmx +=1;
      Tvaraff[ij]=i;          sw += weight[i];
      ij++;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
    }        } /* end of wave */
  }      } /* end of individual */
      }  else if(mle==3){  /* exponential inter-extrapolation */
     cptcoveff=ij-1;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
 /*********** Health Expectancies ****************/          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)              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;          for(d=0; d<dh[mi][i]; d++){
   double age, agelim, hf;            newm=savm;
   double ***p3mat;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
   fprintf(ficreseij,"# Health expectancies\n");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   fprintf(ficreseij,"# Age");            }
   for(i=1; i<=nlstate;i++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for(j=1; j<=nlstate;j++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       fprintf(ficreseij," %1d-%1d",i,j);            savm=oldm;
   fprintf(ficreseij,"\n");            oldm=newm;
           } /* end mult */
   k=1;             /* For example stepm=6 months */        
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */          s1=s[mw[mi][i]][i];
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */          s2=s[mw[mi+1][i]][i];
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          bbh=(double)bh[mi][i]/(double)stepm; 
      nhstepm is the number of hstepm from age to agelim          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 */
      nstepm is the number of stepm from age to agelin.          ipmx +=1;
      Look at hpijx to understand the reason of that which relies in memory size          sw += weight[i];
      and note for a fixed period like k years */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        } /* end of wave */
      survival function given by stepm (the optimization length). Unfortunately it      } /* end of individual */
      means that if the survival funtion is printed only each two years of age and if    }else if (mle==4){  /* ml=4 no inter-extrapolation */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      results. So we changed our mind and took the option of the best precision.        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   */        for(mi=1; mi<= wav[i]-1; mi++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   agelim=AGESUP;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     /* nhstepm age range expressed in number of stepm */            }
     nstepm=(int) rint((agelim-age)*YEARM/stepm);          for(d=0; d<dh[mi][i]; d++){
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */            newm=savm;
     /* if (stepm >= YEARM) hstepm=1;*/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */            for (kk=1; kk<=cptcovage;kk++) {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(i=1; i<=nlstate;i++)            savm=oldm;
       for(j=1; j<=nlstate;j++)            oldm=newm;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          } /* end mult */
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;        
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
     fprintf(ficreseij,"%3.0f",age );          if( s2 > nlstate){ 
     for(i=1; i<=nlstate;i++)            lli=log(out[s1][s2] - savm[s1][s2]);
       for(j=1; j<=nlstate;j++){          }else{
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       }          }
     fprintf(ficreseij,"\n");          ipmx +=1;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          sw += weight[i];
   }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 }  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         } /* end of wave */
 /************ Variance ******************/      } /* end of individual */
 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)    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
 {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /* Variance of health expectancies */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        for(mi=1; mi<= wav[i]-1; mi++){
   double **newm;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double **dnewm,**doldm;            for (j=1;j<=nlstate+ndeath;j++){
   int i, j, nhstepm, hstepm, h, nstepm, kk;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int k, cptcode;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double *xp;            }
   double **gp, **gm;          for(d=0; d<dh[mi][i]; d++){
   double ***gradg, ***trgradg;            newm=savm;
   double ***p3mat;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double age,agelim, hf;            for (kk=1; kk<=cptcovage;kk++) {
   int theta;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
    fprintf(ficresvij,"# Covariances of life expectancies\n");          
   fprintf(ficresvij,"# Age");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for(i=1; i<=nlstate;i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(j=1; j<=nlstate;j++)            savm=oldm;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            oldm=newm;
   fprintf(ficresvij,"\n");          } /* end mult */
         
   xp=vector(1,npar);          s1=s[mw[mi][i]][i];
   dnewm=matrix(1,nlstate,1,npar);          s2=s[mw[mi+1][i]][i];
   doldm=matrix(1,nlstate,1,nlstate);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
            ipmx +=1;
   kk=1;             /* For example stepm=6 months */          sw += weight[i];
   hstepm=kk*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */          /*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]);*/
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        } /* end of wave */
      nhstepm is the number of hstepm from age to agelim      } /* end of individual */
      nstepm is the number of stepm from age to agelin.    } /* End of if */
      Look at hpijx to understand the reason of that which relies in memory size    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
      and note for a fixed period like k years */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      survival function given by stepm (the optimization length). Unfortunately it    return -l;
      means that if the survival funtion is printed only each two years of age and if  }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  
      results. So we changed our mind and took the option of the best precision.  /*************** log-likelihood *************/
   */  double funcone( double *x)
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */  {
   agelim = AGESUP;    /* Same as likeli but slower because of a lot of printf and if */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    int i, ii, j, k, mi, d, kk;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    double **out;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double lli; /* Individual log likelihood */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    double llt;
     gp=matrix(0,nhstepm,1,nlstate);    int s1, s2;
     gm=matrix(0,nhstepm,1,nlstate);    double bbh, survp;
     /*extern weight */
     for(theta=1; theta <=npar; theta++){    /* We are differentiating ll according to initial status */
       for(i=1; i<=npar; i++){ /* Computes gradient */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    /*for(i=1;i<imx;i++) 
       }      printf(" %d\n",s[4][i]);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    cov[1]=1.;
   
       if (popbased==1) {    for(k=1; k<=nlstate; k++) ll[k]=0.;
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
        for(mi=1; mi<= wav[i]-1; mi++){
       for(j=1; j<= nlstate; j++){        for (ii=1;ii<=nlstate+ndeath;ii++)
         for(h=0; h<=nhstepm; h++){          for (j=1;j<=nlstate+ndeath;j++){
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }          }
       }        for(d=0; d<dh[mi][i]; d++){
              newm=savm;
       for(i=1; i<=npar; i++) /* Computes gradient */          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          for (kk=1; kk<=cptcovage;kk++) {
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       if (popbased==1) {                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         for(i=1; i<=nlstate;i++)          savm=oldm;
           prlim[i][i]=probs[(int)age][i][ij];          oldm=newm;
       }        } /* end mult */
         
       for(j=1; j<= nlstate; j++){        s1=s[mw[mi][i]][i];
         for(h=0; h<=nhstepm; h++){        s2=s[mw[mi+1][i]][i];
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        bbh=(double)bh[mi][i]/(double)stepm; 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        /* bias is positive if real duration
         }         * is higher than the multiple of stepm and negative otherwise.
       }         */
         if( s2 > nlstate && (mle <5) ){  /* Jackson */
       for(j=1; j<= nlstate; j++)          lli=log(out[s1][s2] - savm[s1][s2]);
         for(h=0; h<=nhstepm; h++){        } else if  (s2==-2) {
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          for (j=1,survp=0. ; j<=nlstate; j++) 
         }            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     } /* End theta */          lli= log(survp);
         }else if (mle==1){
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
     for(h=0; h<=nhstepm; h++)          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       for(j=1; j<=nlstate;j++)        } else if(mle==3){  /* exponential inter-extrapolation */
         for(theta=1; theta <=npar; theta++)          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 */
           trgradg[h][j][theta]=gradg[h][theta][j];        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           lli=log(out[s1][s2]); /* Original formula */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
     for(i=1;i<=nlstate;i++)          lli=log(out[s1][s2]); /* Original formula */
       for(j=1;j<=nlstate;j++)        } /* End of if */
         vareij[i][j][(int)age] =0.;        ipmx +=1;
         sw += weight[i];
     for(h=0;h<=nhstepm;h++){        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(k=0;k<=nhstepm;k++){        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]); 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        if(globpr){
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
         for(i=1;i<=nlstate;i++)   %11.6f %11.6f %11.6f ", \
           for(j=1;j<=nlstate;j++)                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
       }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     }            llt +=ll[k]*gipmx/gsw;
             fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     fprintf(ficresvij,"%.0f ",age );          }
     for(i=1; i<=nlstate;i++)          fprintf(ficresilk," %10.6f\n", -llt);
       for(j=1; j<=nlstate;j++){        }
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);      } /* end of wave */
       }    } /* end of individual */
     fprintf(ficresvij,"\n");    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     free_matrix(gp,0,nhstepm,1,nlstate);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     free_matrix(gm,0,nhstepm,1,nlstate);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    if(globpr==0){ /* First time we count the contributions and weights */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      gipmx=ipmx;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      gsw=sw;
   } /* End age */    }
      return -l;
   free_vector(xp,1,npar);  }
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);  
   /*************** function likelione ***********/
 }  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   {
 /************ Variance of prevlim ******************/    /* This routine should help understanding what is done with 
 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)       the selection of individuals/waves and
 {       to check the exact contribution to the likelihood.
   /* Variance of prevalence limit */       Plotting could be done.
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/     */
   double **newm;    int k;
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm;    if(*globpri !=0){ /* Just counts and sums, no printings */
   int k, cptcode;      strcpy(fileresilk,"ilk"); 
   double *xp;      strcat(fileresilk,fileres);
   double *gp, *gm;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   double **gradg, **trgradg;        printf("Problem with resultfile: %s\n", fileresilk);
   double age,agelim;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   int theta;      }
          fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   fprintf(ficresvpl,"# Age");      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   for(i=1; i<=nlstate;i++)      for(k=1; k<=nlstate; k++) 
       fprintf(ficresvpl," %1d-%1d",i,i);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   fprintf(ficresvpl,"\n");      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);    *fretone=(*funcone)(p);
   doldm=matrix(1,nlstate,1,nlstate);    if(*globpri !=0){
        fclose(ficresilk);
   hstepm=1*YEARM; /* Every year of age */      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      fflush(fichtm); 
   agelim = AGESUP;    } 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    return;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  }
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
     gradg=matrix(1,npar,1,nlstate);  /*********** Maximum Likelihood Estimation ***************/
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
     for(theta=1; theta <=npar; theta++){    int i,j, iter;
       for(i=1; i<=npar; i++){ /* Computes gradient */    double **xi;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double fret;
       }    double fretone; /* Only one call to likelihood */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /*  char filerespow[FILENAMELENGTH];*/
       for(i=1;i<=nlstate;i++)    xi=matrix(1,npar,1,npar);
         gp[i] = prlim[i][i];    for (i=1;i<=npar;i++)
          for (j=1;j<=npar;j++)
       for(i=1; i<=npar; i++) /* Computes gradient */        xi[i][j]=(i==j ? 1.0 : 0.0);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    strcpy(filerespow,"pow"); 
       for(i=1;i<=nlstate;i++)    strcat(filerespow,fileres);
         gm[i] = prlim[i][i];    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
       for(i=1;i<=nlstate;i++)      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    }
     } /* End theta */    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
     trgradg =matrix(1,nlstate,1,npar);      for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     for(j=1; j<=nlstate;j++)    fprintf(ficrespow,"\n");
       for(theta=1; theta <=npar; theta++)  
         trgradg[j][theta]=gradg[theta][j];    powell(p,xi,npar,ftol,&iter,&fret,func);
   
     for(i=1;i<=nlstate;i++)    free_matrix(xi,1,npar,1,npar);
       varpl[i][(int)age] =0.;    fclose(ficrespow);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for(i=1;i<=nlstate;i++)    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  
   }
     fprintf(ficresvpl,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)  /**** Computes Hessian and covariance matrix ***/
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     fprintf(ficresvpl,"\n");  {
     free_vector(gp,1,nlstate);    double  **a,**y,*x,pd;
     free_vector(gm,1,nlstate);    double **hess;
     free_matrix(gradg,1,npar,1,nlstate);    int i, j,jk;
     free_matrix(trgradg,1,nlstate,1,npar);    int *indx;
   } /* End age */  
     double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   free_vector(xp,1,npar);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   free_matrix(doldm,1,nlstate,1,npar);    void lubksb(double **a, int npar, int *indx, double b[]) ;
   free_matrix(dnewm,1,nlstate,1,nlstate);    void ludcmp(double **a, int npar, int *indx, double *d) ;
     double gompertz(double p[]);
 }    hess=matrix(1,npar,1,npar);
   
 /************ Variance of one-step probabilities  ******************/    printf("\nCalculation of the hessian matrix. Wait...\n");
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
 {    for (i=1;i<=npar;i++){
   int i, j;      printf("%d",i);fflush(stdout);
   int k=0, cptcode;      fprintf(ficlog,"%d",i);fflush(ficlog);
   double **dnewm,**doldm;     
   double *xp;       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   double *gp, *gm;      
   double **gradg, **trgradg;      /*  printf(" %f ",p[i]);
   double age,agelim, cov[NCOVMAX];          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   int theta;    }
   char fileresprob[FILENAMELENGTH];    
     for (i=1;i<=npar;i++) {
   strcpy(fileresprob,"prob");      for (j=1;j<=npar;j++)  {
   strcat(fileresprob,fileres);        if (j>i) { 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          printf(".%d%d",i,j);fflush(stdout);
     printf("Problem with resultfile: %s\n", fileresprob);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   }          hess[i][j]=hessij(p,delti,i,j,func,npar);
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          
            hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
   xp=vector(1,npar);        }
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      }
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    }
      printf("\n");
   cov[1]=1;    fprintf(ficlog,"\n");
   for (age=bage; age<=fage; age ++){  
     cov[2]=age;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     gradg=matrix(1,npar,1,9);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     trgradg=matrix(1,9,1,npar);    
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    a=matrix(1,npar,1,npar);
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    y=matrix(1,npar,1,npar);
        x=vector(1,npar);
     for(theta=1; theta <=npar; theta++){    indx=ivector(1,npar);
       for(i=1; i<=npar; i++)    for (i=1;i<=npar;i++)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
          ludcmp(a,npar,indx,&pd);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  
        for (j=1;j<=npar;j++) {
       k=0;      for (i=1;i<=npar;i++) x[i]=0;
       for(i=1; i<= (nlstate+ndeath); i++){      x[j]=1;
         for(j=1; j<=(nlstate+ndeath);j++){      lubksb(a,npar,indx,x);
            k=k+1;      for (i=1;i<=npar;i++){ 
           gp[k]=pmmij[i][j];        matcov[i][j]=x[i];
         }      }
       }    }
   
       for(i=1; i<=npar; i++)    printf("\n#Hessian matrix#\n");
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    fprintf(ficlog,"\n#Hessian matrix#\n");
        for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        printf("%.3e ",hess[i][j]);
       k=0;        fprintf(ficlog,"%.3e ",hess[i][j]);
       for(i=1; i<=(nlstate+ndeath); i++){      }
         for(j=1; j<=(nlstate+ndeath);j++){      printf("\n");
           k=k+1;      fprintf(ficlog,"\n");
           gm[k]=pmmij[i][j];    }
         }  
       }    /* Recompute Inverse */
          for (i=1;i<=npar;i++)
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      ludcmp(a,npar,indx,&pd);
     }  
     /*  printf("\n#Hessian matrix recomputed#\n");
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  
       for(theta=1; theta <=npar; theta++)    for (j=1;j<=npar;j++) {
       trgradg[j][theta]=gradg[theta][j];      for (i=1;i<=npar;i++) x[i]=0;
        x[j]=1;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      lubksb(a,npar,indx,x);
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);      for (i=1;i<=npar;i++){ 
         y[i][j]=x[i];
      pmij(pmmij,cov,ncovmodel,x,nlstate);        printf("%.3e ",y[i][j]);
         fprintf(ficlog,"%.3e ",y[i][j]);
      k=0;      }
      for(i=1; i<=(nlstate+ndeath); i++){      printf("\n");
        for(j=1; j<=(nlstate+ndeath);j++){      fprintf(ficlog,"\n");
          k=k+1;    }
          gm[k]=pmmij[i][j];    */
         }  
      }    free_matrix(a,1,npar,1,npar);
          free_matrix(y,1,npar,1,npar);
      /*printf("\n%d ",(int)age);    free_vector(x,1,npar);
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    free_ivector(indx,1,npar);
            free_matrix(hess,1,npar,1,npar);
   
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  
      }*/  }
   
   fprintf(ficresprob,"\n%d ",(int)age);  /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  {
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    int i;
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    int l=1, lmax=20;
   }    double k1,k2;
     double p2[NPARMAX+1];
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    double res;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    double fx;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    int k=0,kmax=10;
 }    double l1;
  free_vector(xp,1,npar);  
 fclose(ficresprob);    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
 }    for(l=0 ; l <=lmax; l++){
       l1=pow(10,l);
 /******************* Printing html file ***********/      delts=delt;
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      for(k=1 ; k <kmax; k=k+1){
  int lastpass, int stepm, int weightopt, char model[],\        delt = delta*(l1*k);
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \        p2[theta]=x[theta] +delt;
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\        k1=func(p2)-fx;
  char version[], int popforecast ){        p2[theta]=x[theta]-delt;
   int jj1, k1, i1, cpt;        k2=func(p2)-fx;
   FILE *fichtm;        /*res= (k1-2.0*fx+k2)/delt/delt; */
   /*char optionfilehtm[FILENAMELENGTH];*/        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
   strcpy(optionfilehtm,optionfile);  #ifdef DEBUG
   strcat(optionfilehtm,".htm");        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);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        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);
     printf("Problem with %s \n",optionfilehtm), exit(0);  #endif
   }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
  fprintf(fichtm,"<body> <font size=\"2\">Imach, Version %s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n          k=kmax;
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n        }
 \n        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 Total number of observations=%d <br>\n          k=kmax; l=lmax*10.;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n        }
 <hr  size=\"2\" color=\"#EC5E5E\">        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
  <ul><li>Outputs files<br>\n          delts=delt;
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n        }
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n      }
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    }
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n    delti[theta]=delts;
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n    return res; 
  - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    
   }
  fprintf(fichtm,"\n  
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
  - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>\n  {
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n    int i;
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres);    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
  if(popforecast==1) fprintf(fichtm,"\n    double p2[NPARMAX+1];
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    int k;
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n  
         <br>",fileres,fileres,fileres,fileres);    fx=func(x);
  else    for (k=1; k<=2; k++) {
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);      for (i=1;i<=npar;i++) p2[i]=x[i];
 fprintf(fichtm," <li>Graphs</li><p>");      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
  m=cptcoveff;      k1=func(p2)-fx;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    
       p2[thetai]=x[thetai]+delti[thetai]/k;
  jj1=0;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
  for(k1=1; k1<=m;k1++){      k2=func(p2)-fx;
    for(i1=1; i1<=ncodemax[k1];i1++){    
        jj1++;      p2[thetai]=x[thetai]-delti[thetai]/k;
        if (cptcovn > 0) {      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      k3=func(p2)-fx;
          for (cpt=1; cpt<=cptcoveff;cpt++)    
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      p2[thetai]=x[thetai]-delti[thetai]/k;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        }      k4=func(p2)-fx;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      #ifdef DEBUG
        for(cpt=1; cpt<nlstate;cpt++){      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);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      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);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  #endif
        }    }
     for(cpt=1; cpt<=nlstate;cpt++) {    return res;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  }
 interval) in state (%d): v%s%d%d.gif <br>  
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    /************** Inverse of matrix **************/
      }  void ludcmp(double **a, int n, int *indx, double *d) 
      for(cpt=1; cpt<=nlstate;cpt++) {  { 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    int i,imax,j,k; 
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    double big,dum,sum,temp; 
      }    double *vv; 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and   
 health expectancies in states (1) and (2): e%s%d.gif<br>    vv=vector(1,n); 
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    *d=1.0; 
 fprintf(fichtm,"\n</body>");    for (i=1;i<=n;i++) { 
    }      big=0.0; 
    }      for (j=1;j<=n;j++) 
 fclose(fichtm);        if ((temp=fabs(a[i][j])) > big) big=temp; 
 }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
 /******************* Gnuplot file **************/    } 
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   strcpy(optionfilegnuplot,optionfilefiname);        a[i][j]=sum; 
   strcat(optionfilegnuplot,".gp.txt");      } 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      big=0.0; 
     printf("Problem with file %s",optionfilegnuplot);      for (i=j;i<=n;i++) { 
   }        sum=a[i][j]; 
         for (k=1;k<j;k++) 
 #ifdef windows          sum -= a[i][k]*a[k][j]; 
     fprintf(ficgp,"cd \"%s\" \n",pathc);        a[i][j]=sum; 
 #endif        if ( (dum=vv[i]*fabs(sum)) >= big) { 
 m=pow(2,cptcoveff);          big=dum; 
            imax=i; 
  /* 1eme*/        } 
   for (cpt=1; cpt<= nlstate ; cpt ++) {      } 
    for (k1=1; k1<= m ; k1 ++) {      if (j != imax) { 
         for (k=1;k<=n;k++) { 
 #ifdef windows          dum=a[imax][k]; 
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);          a[imax][k]=a[j][k]; 
 #endif          a[j][k]=dum; 
 #ifdef unix        } 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);        *d = -(*d); 
 #endif        vv[imax]=vv[j]; 
       } 
 for (i=1; i<= nlstate ; i ++) {      indx[j]=imax; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      if (a[j][j] == 0.0) a[j][j]=TINY; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      if (j != n) { 
 }        dum=1.0/(a[j][j]); 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     for (i=1; i<= nlstate ; i ++) {      } 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    free_vector(vv,1,n);  /* Doesn't work */
 }  ;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  } 
      for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  void lubksb(double **a, int n, int *indx, double b[]) 
   else fprintf(ficgp," \%%*lf (\%%*lf)");  { 
 }      int i,ii=0,ip,j; 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    double sum; 
 #ifdef unix   
 fprintf(ficgp,"\nset ter gif small size 400,300");    for (i=1;i<=n;i++) { 
 #endif      ip=indx[i]; 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      sum=b[ip]; 
    }      b[ip]=b[i]; 
   }      if (ii) 
   /*2 eme*/        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else if (sum) ii=i; 
   for (k1=1; k1<= m ; k1 ++) {      b[i]=sum; 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);    } 
        for (i=n;i>=1;i--) { 
     for (i=1; i<= nlstate+1 ; i ++) {      sum=b[i]; 
       k=2*i;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      b[i]=sum/a[i][i]; 
       for (j=1; j<= nlstate+1 ; j ++) {    } 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }    void pstamp(FILE *fichier)
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");  {
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);  }
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  /************ Frequencies ********************/
         else fprintf(ficgp," \%%*lf (\%%*lf)");  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[])
 }    {  /* Some frequencies */
       fprintf(ficgp,"\" t\"\" w l 0,");    
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    int i, m, jk, k1,i1, j1, bool, z1,j;
       for (j=1; j<= nlstate+1 ; j ++) {    int first;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double ***freq; /* Frequencies */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double *pp, **prop;
 }      double pos,posprop, k2, dateintsum=0,k2cpt=0;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    char fileresp[FILENAMELENGTH];
       else fprintf(ficgp,"\" t\"\" w l 0,");    
     }    pp=vector(1,nlstate);
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    prop=matrix(1,nlstate,iagemin,iagemax+3);
   }    strcpy(fileresp,"p");
      strcat(fileresp,fileres);
   /*3eme*/    if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
   for (k1=1; k1<= m ; k1 ++) {      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     for (cpt=1; cpt<= nlstate ; cpt ++) {      exit(0);
       k=2+nlstate*(cpt-1);    }
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
       for (i=1; i< nlstate ; i ++) {    j1=0;
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);    
       }    j=cptcoveff;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     }  
     }    first=1;
    
   /* CV preval stat */    for(k1=1; k1<=j;k1++){
     for (k1=1; k1<= m ; k1 ++) {      for(i1=1; i1<=ncodemax[k1];i1++){
     for (cpt=1; cpt<nlstate ; cpt ++) {        j1++;
       k=3;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);          scanf("%d", i);*/
         for (i=-5; i<=nlstate+ndeath; i++)  
       for (i=1; i< nlstate ; i ++)          for (jk=-5; jk<=nlstate+ndeath; jk++)  
         fprintf(ficgp,"+$%d",k+i+1);            for(m=iagemin; m <= iagemax+3; m++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              freq[i][jk][m]=0;
        
       l=3+(nlstate+ndeath)*cpt;      for (i=1; i<=nlstate; i++)  
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        for(m=iagemin; m <= iagemax+3; m++)
       for (i=1; i< nlstate ; i ++) {          prop[i][m]=0;
         l=3+(nlstate+ndeath)*cpt;        
         fprintf(ficgp,"+$%d",l+i+1);        dateintsum=0;
       }        k2cpt=0;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          for (i=1; i<=imx; i++) {
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          bool=1;
     }          if  (cptcovn>0) {
   }              for (z1=1; z1<=cptcoveff; z1++) 
                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   /* proba elementaires */                bool=0;
    for(i=1,jk=1; i <=nlstate; i++){          }
     for(k=1; k <=(nlstate+ndeath); k++){          if (bool==1){
       if (k != i) {            for(m=firstpass; m<=lastpass; m++){
         for(j=1; j <=ncovmodel; j++){              k2=anint[m][i]+(mint[m][i]/12.);
                      /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           jk++;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           fprintf(ficgp,"\n");                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];
     }                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     }                }
                 
     for(jk=1; jk <=m; jk++) {                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);                  dateintsum=dateintsum+k2;
    i=1;                  k2cpt++;
    for(k2=1; k2<=nlstate; k2++) {                }
      k3=i;                /*}*/
      for(k=1; k<=(nlstate+ndeath); k++) {            }
        if (k != k2){          }
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        }
 ij=1;         
         for(j=3; j <=ncovmodel; j++) {        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        pstamp(ficresp);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        if  (cptcovn>0) {
             ij++;          fprintf(ficresp, "\n#********** Variable "); 
           }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           else          fprintf(ficresp, "**********\n#");
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        }
         }        for(i=1; i<=nlstate;i++) 
           fprintf(ficgp,")/(1");          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
                fprintf(ficresp, "\n");
         for(k1=1; k1 <=nlstate; k1++){          
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        for(i=iagemin; i <= iagemax+3; i++){
 ij=1;          if(i==iagemax+3){
           for(j=3; j <=ncovmodel; j++){            fprintf(ficlog,"Total");
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          }else{
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            if(first==1){
             ij++;              first=0;
           }              printf("See log file for details...\n");
           else            }
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            fprintf(ficlog,"Age %d", i);
           }          }
           fprintf(ficgp,")");          for(jk=1; jk <=nlstate ; jk++){
         }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);              pp[jk] += freq[jk][m][i]; 
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          }
         i=i+ncovmodel;          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){
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);              if(first==1){
    }              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                  }
   fclose(ficgp);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 }  /* end gnuplot */            }else{
               if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 /*************** Moving average **************/              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){            }
           }
   int i, cpt, cptcod;  
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)          for(jk=1; jk <=nlstate ; jk++){
       for (i=1; i<=nlstate;i++)            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)              pp[jk] += freq[jk][m][i];
           mobaverage[(int)agedeb][i][cptcod]=0.;          }       
              for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){            pos += pp[jk];
       for (i=1; i<=nlstate;i++){            posprop += prop[jk][i];
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          }
           for (cpt=0;cpt<=4;cpt++){          for(jk=1; jk <=nlstate ; jk++){
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];            if(pos>=1.e-5){
           }              if(first==1)
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         }              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       }            }else{
     }              if(first==1)
                    printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
             if( i <= iagemax){
 /************** Forecasting ******************/              if(pos>=1.e-5){
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                  /*probs[i][jk][j1]= pp[jk]/pos;*/
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   int *popage;              }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;              else
   double *popeffectif,*popcount;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   double ***p3mat;            }
   char fileresf[FILENAMELENGTH];          }
           
  agelim=AGESUP;          for(jk=-1; jk <=nlstate+ndeath; jk++)
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              if(first==1)
                  printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                  fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   strcpy(fileresf,"f");              }
   strcat(fileresf,fileres);          if(i <= iagemax)
   if((ficresf=fopen(fileresf,"w"))==NULL) {            fprintf(ficresp,"\n");
     printf("Problem with forecast resultfile: %s\n", fileresf);          if(first==1)
   }            printf("Others in log...\n");
   printf("Computing forecasting: result on file '%s' \n", fileresf);          fprintf(ficlog,"\n");
         }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      }
     }
   if (mobilav==1) {    dateintmean=dateintsum/k2cpt; 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
     movingaverage(agedeb, fage, ageminpar, mobaverage);    fclose(ficresp);
   }    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   if (stepm<=12) stepsize=1;    /* End of Freq */
    }
   agelim=AGESUP;  
    /************ Prevalence ********************/
   hstepm=1;  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)
   hstepm=hstepm/stepm;  {  
   yp1=modf(dateintmean,&yp);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   anprojmean=yp;       in each health status at the date of interview (if between dateprev1 and dateprev2).
   yp2=modf((yp1*12),&yp);       We still use firstpass and lastpass as another selection.
   mprojmean=yp;    */
   yp1=modf((yp2*30.5),&yp);   
   jprojmean=yp;    int i, m, jk, k1, i1, j1, bool, z1,j;
   if(jprojmean==0) jprojmean=1;    double ***freq; /* Frequencies */
   if(mprojmean==0) jprojmean=1;    double *pp, **prop;
      double pos,posprop; 
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    double  y2; /* in fractional years */
      int iagemin, iagemax;
   for(cptcov=1;cptcov<=i2;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    iagemin= (int) agemin;
       k=k+1;    iagemax= (int) agemax;
       fprintf(ficresf,"\n#******");    /*pp=vector(1,nlstate);*/
       for(j=1;j<=cptcoveff;j++) {    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       }    j1=0;
       fprintf(ficresf,"******\n");    
       fprintf(ficresf,"# StartingAge FinalAge");    j=cptcoveff;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
          
          for(k1=1; k1<=j;k1++){
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      for(i1=1; i1<=ncodemax[k1];i1++){
         fprintf(ficresf,"\n");        j1++;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);          
         for (i=1; i<=nlstate; i++)  
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          for(m=iagemin; m <= iagemax+3; m++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            prop[i][m]=0.0;
           nhstepm = nhstepm/hstepm;       
                  for (i=1; i<=imx; i++) { /* Each individual */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          bool=1;
           oldm=oldms;savm=savms;          if  (cptcovn>0) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for (z1=1; z1<=cptcoveff; z1++) 
                      if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           for (h=0; h<=nhstepm; h++){                bool=0;
             if (h==(int) (calagedate+YEARM*cpt)) {          } 
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);          if (bool==1) { 
             }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
             for(j=1; j<=nlstate+ndeath;j++) {              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
               kk1=0.;kk2=0;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
               for(i=1; i<=nlstate;i++) {                              if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if (mobilav==1)                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                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); 
                 else {                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                 }                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                                  prop[s[m][i]][iagemax+3] += weight[i]; 
               }                } 
               if (h==(int)(calagedate+12*cpt)){              }
                 fprintf(ficresf," %.3f", kk1);            } /* end selection of waves */
                                  }
               }        }
             }        for(i=iagemin; i <= iagemax+3; i++){  
           }          
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         }            posprop += prop[jk][i]; 
       }          } 
     }  
   }          for(jk=1; jk <=nlstate ; jk++){     
                    if( i <=  iagemax){ 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              if(posprop>=1.e-5){ 
                 probs[i][jk][j1]= prop[jk][i]/posprop;
   fclose(ficresf);              } else
 }                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
 /************** 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){          }/* end jk */ 
          }/* end i */ 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      } /* end i1 */
   int *popage;    } /* end k1 */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    
   double *popeffectif,*popcount;    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   double ***p3mat,***tabpop,***tabpopprev;    /*free_vector(pp,1,nlstate);*/
   char filerespop[FILENAMELENGTH];    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /************* Waves Concatenation ***************/
   agelim=AGESUP;  
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;  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)
    {
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         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
   strcpy(filerespop,"pop");       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   strcat(filerespop,fileres);       and mw[mi+1][i]. dh depends on stepm.
   if((ficrespop=fopen(filerespop,"w"))==NULL) {       */
     printf("Problem with forecast resultfile: %s\n", filerespop);  
   }    int i, mi, m;
   printf("Computing forecasting: result on file '%s' \n", filerespop);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
        double sum=0., jmean=0.;*/
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    int first;
     int j, k=0,jk, ju, jl;
   if (mobilav==1) {    double sum=0.;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    first=0;
     movingaverage(agedeb, fage, ageminpar, mobaverage);    jmin=1e+5;
   }    jmax=-1;
     jmean=0.;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    for(i=1; i<=imx; i++){
   if (stepm<=12) stepsize=1;      mi=0;
        m=firstpass;
   agelim=AGESUP;      while(s[m][i] <= nlstate){
          if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
   hstepm=1;          mw[++mi][i]=m;
   hstepm=hstepm/stepm;        if(m >=lastpass)
            break;
   if (popforecast==1) {        else
     if((ficpop=fopen(popfile,"r"))==NULL) {          m++;
       printf("Problem with population file : %s\n",popfile);exit(0);      }/* end while */
     }      if (s[m][i] > nlstate){
     popage=ivector(0,AGESUP);        mi++;     /* Death is another wave */
     popeffectif=vector(0,AGESUP);        /* if(mi==0)  never been interviewed correctly before death */
     popcount=vector(0,AGESUP);           /* Only death is a correct wave */
            mw[mi][i]=m;
     i=1;        }
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;  
          wav[i]=mi;
     imx=i;      if(mi==0){
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];        nbwarn++;
   }        if(first==0){
           printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   for(cptcov=1;cptcov<=i2;cptcov++){          first=1;
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        }
       k=k+1;        if(first==1){
       fprintf(ficrespop,"\n#******");          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
       for(j=1;j<=cptcoveff;j++) {        }
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      } /* end mi==0 */
       }    } /* End individuals */
       fprintf(ficrespop,"******\n");  
       fprintf(ficrespop,"# Age");    for(i=1; i<=imx; i++){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      for(mi=1; mi<wav[i];mi++){
       if (popforecast==1)  fprintf(ficrespop," [Population]");        if (stepm <=0)
                dh[mi][i]=1;
       for (cpt=0; cpt<=0;cpt++) {        else{
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                    if (agedc[i] < 2*AGESUP) {
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              if(j==0) j=1;  /* Survives at least one month after exam */
           nhstepm = nhstepm/hstepm;              else if(j<0){
                          nberr++;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                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]);
           oldm=oldms;savm=savms;                j=1; /* Temporary Dangerous patch */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                  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);
                        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]);
           for (h=0; h<=nhstepm; h++){                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);
             if (h==(int) (calagedate+YEARM*cpt)) {              }
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);              k=k+1;
             }              if (j >= jmax){
             for(j=1; j<=nlstate+ndeath;j++) {                jmax=j;
               kk1=0.;kk2=0;                ijmax=i;
               for(i=1; i<=nlstate;i++) {                            }
                 if (mobilav==1)              if (j <= jmin){
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                jmin=j;
                 else {                ijmin=i;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];              }
                 }              sum=sum+j;
               }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               if (h==(int)(calagedate+12*cpt)){              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;            }
                   /*fprintf(ficrespop," %.3f", kk1);          }
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/          else{
               }            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]); */
             for(i=1; i<=nlstate;i++){  
               kk1=0.;            k=k+1;
                 for(j=1; j<=nlstate;j++){            if (j >= jmax) {
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];              jmax=j;
                 }              ijmax=i;
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];            }
             }            else if (j <= jmin){
               jmin=j;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)              ijmin=i;
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);            }
           }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            /*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]);*/
         }            if(j<0){
       }              nberr++;
                printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   /******/              fprintf(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]);
             }
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {            sum=sum+j;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          jk= j/stepm;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          jl= j -jk*stepm;
           nhstepm = nhstepm/hstepm;          ju= j -(jk+1)*stepm;
                    if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            if(jl==0){
           oldm=oldms;savm=savms;              dh[mi][i]=jk;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                bh[mi][i]=0;
           for (h=0; h<=nhstepm; h++){            }else{ /* We want a negative bias in order to only have interpolation ie
             if (h==(int) (calagedate+YEARM*cpt)) {                    * at the price of an extra matrix product in likelihood */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);              dh[mi][i]=jk+1;
             }              bh[mi][i]=ju;
             for(j=1; j<=nlstate+ndeath;j++) {            }
               kk1=0.;kk2=0;          }else{
               for(i=1; i<=nlstate;i++) {                          if(jl <= -ju){
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                  dh[mi][i]=jk;
               }              bh[mi][i]=jl;       /* bias is positive if real duration
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);                                   * is higher than the multiple of stepm and negative otherwise.
             }                                   */
           }            }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            else{
         }              dh[mi][i]=jk+1;
       }              bh[mi][i]=ju;
    }            }
   }            if(dh[mi][i]==0){
                dh[mi][i]=1; /* At least one step */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              bh[mi][i]=ju; /* At least one step */
               /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
   if (popforecast==1) {            }
     free_ivector(popage,0,AGESUP);          } /* end if mle */
     free_vector(popeffectif,0,AGESUP);        }
     free_vector(popcount,0,AGESUP);      } /* end wave */
   }    }
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    jmean=sum/k;
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    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(ficrespop);    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);
 }   }
   
 /***********************************************/  /*********** Tricode ****************************/
 /**************** Main Program *****************/  void tricode(int *Tvar, int **nbcode, int imx)
 /***********************************************/  {
     
 int main(int argc, char *argv[])    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
 {  
     int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    int cptcode=0;
   double agedeb, agefin,hf;    cptcoveff=0; 
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;   
     for (k=0; k<maxncov; k++) Ndum[k]=0;
   double fret;    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
   double **xi,tmp,delta;  
     for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate */
   double dum; /* Dummy variable */      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   double ***p3mat;                                 modality*/ 
   int *indx;        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual, might be -1*/
   char line[MAXLINE], linepar[MAXLINE];        Ndum[ij]++; /*counts the occurence of this modality */
   char title[MAXLINE];        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];        if (ij > cptcode) cptcode=ij; /* getting the maximum value of the modality of the covariate  (should be 0 or 1 now) 
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];                                         Tvar[j]. If V=sex and male is 0 and 
                                           female is 1, then  cptcode=1.*/
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];      }
   
   char filerest[FILENAMELENGTH];      for (i=0; i<=cptcode; i++) { /* i=-1 ?*/
   char fileregp[FILENAMELENGTH];        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariate. In fact ncodemax[j]=2 (dichotom. variables only) but it can be more */
   char popfile[FILENAMELENGTH];      } /* Ndum[-1] number of undefined modalities */
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  
   int firstobs=1, lastobs=10;      ij=1; 
   int sdeb, sfin; /* Status at beginning and end */      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */
   int c,  h , cpt,l;        for (k=0; k<= maxncov; k++) { /* k=-1 ?*/
   int ju,jl, mi;          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;                                       k is a modality. If we have model=V1+V1*sex 
   int mobilav=0,popforecast=0;                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   int hstepm, nhstepm;            ij++;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;          }
           if (ij > ncodemax[j]) break; 
   double bage, fage, age, agelim, agebase;        }  
   double ftolpl=FTOL;      } 
   double **prlim;    }  
   double *severity;  
   double ***param; /* Matrix of parameters */   for (k=0; k< maxncov; k++) Ndum[k]=0;
   double  *p;  
   double **matcov; /* Matrix of covariance */   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
   double ***delti3; /* Scale */     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   double *delti; /* Scale */     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
   double ***eij, ***vareij;     Ndum[ij]++;
   double **varpl; /* Variances of prevalence limits by age */   }
   double *epj, vepp;  
   double kk1, kk2;   ij=1;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;   for (i=1; i<= maxncov; i++) {
       if((Ndum[i]!=0) && (i<=ncovcol)){
        Tvaraff[ij]=i; /*For printing */
   char version[80]="Imach version 0.8a, March 2002, INED-EUROREVES ";       ij++;
   char *alph[]={"a","a","b","c","d","e"}, str[4];     }
    }
    ij--;
   char z[1]="c", occ;   cptcoveff=ij; /*Number of simple covariates*/
 #include <sys/time.h>  }
 #include <time.h>  
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  /*********** Health Expectancies ****************/
    
   /* long total_usecs;  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   struct timeval start_time, end_time;  
    {
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    /* Health expectancies, no variances */
   getcwd(pathcd, size);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
     int nhstepma, nstepma; /* Decreasing with age */
   printf("\n%s",version);    double age, agelim, hf;
   if(argc <=1){    double ***p3mat;
     printf("\nEnter the parameter file name: ");    double eip;
     scanf("%s",pathtot);  
   }    pstamp(ficreseij);
   else{    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     strcpy(pathtot,argv[1]);    fprintf(ficreseij,"# Age");
   }    for(i=1; i<=nlstate;i++){
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/      for(j=1; j<=nlstate;j++){
   /*cygwin_split_path(pathtot,path,optionfile);        fprintf(ficreseij," e%1d%1d ",i,j);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      }
   /* cutv(path,optionfile,pathtot,'\\');*/      fprintf(ficreseij," e%1d. ",i);
     }
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    fprintf(ficreseij,"\n");
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  
   chdir(path);    
   replace(pathc,path);    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
 /*-------- arguments in the command line --------*/    }
     else  hstepm=estepm;   
   strcpy(fileres,"r");    /* We compute the life expectancy from trapezoids spaced every estepm months
   strcat(fileres, optionfilefiname);     * This is mainly to measure the difference between two models: for example
   strcat(fileres,".txt");    /* Other files have txt extension */     * 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 
   /*---------arguments file --------*/     * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     printf("Problem with optionfile %s\n",optionfile);     * to compare the new estimate of Life expectancy with the same linear 
     goto end;     * hypothesis. A more precise result, taking into account a more precise
   }     * curvature will be obtained if estepm is as small as stepm. */
   
   strcpy(filereso,"o");    /* For example we decided to compute the life expectancy with the smallest unit */
   strcat(filereso,fileres);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   if((ficparo=fopen(filereso,"w"))==NULL) {       nhstepm is the number of hstepm from age to agelim 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;       nstepm is the number of stepm from age to agelin. 
   }       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
   /* Reads comments: lines beginning with '#' */    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   while((c=getc(ficpar))=='#' && c!= EOF){       survival function given by stepm (the optimization length). Unfortunately it
     ungetc(c,ficpar);       means that if the survival funtion is printed only each two years of age and if
     fgets(line, MAXLINE, ficpar);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     puts(line);       results. So we changed our mind and took the option of the best precision.
     fputs(line,ficparo);    */
   }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   ungetc(c,ficpar);  
     agelim=AGESUP;
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    /* If stepm=6 months */
   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);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   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);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
 while((c=getc(ficpar))=='#' && c!= EOF){      
     ungetc(c,ficpar);  /* nhstepm age range expressed in number of stepm */
     fgets(line, MAXLINE, ficpar);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     puts(line);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     fputs(line,ficparo);    /* if (stepm >= YEARM) hstepm=1;*/
   }    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   ungetc(c,ficpar);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    
        for (age=bage; age<=fage; age ++){ 
   covar=matrix(0,NCOVMAX,1,n);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   cptcovn=0;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      /* if (stepm >= YEARM) hstepm=1;*/
       nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      /* If stepm=6 months */
        /* Computed by stepm unit matrices, product of hstepma matrices, stored
   /* Read guess parameters */         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   /* Reads comments: lines beginning with '#' */      
   while((c=getc(ficpar))=='#' && c!= EOF){      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     ungetc(c,ficpar);      
     fgets(line, MAXLINE, ficpar);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     puts(line);      
     fputs(line,ficparo);      printf("%d|",(int)age);fflush(stdout);
   }      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   ungetc(c,ficpar);      
        /* Computing expectancies */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      for(i=1; i<=nlstate;i++)
     for(i=1; i <=nlstate; i++)        for(j=1; j<=nlstate;j++)
     for(j=1; j <=nlstate+ndeath-1; j++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       fprintf(ficparo,"%1d%1d",i1,j1);            
       printf("%1d%1d",i,j);            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);          }
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);      fprintf(ficreseij,"%3.0f",age );
       }      for(i=1; i<=nlstate;i++){
       fscanf(ficpar,"\n");        eip=0;
       printf("\n");        for(j=1; j<=nlstate;j++){
       fprintf(ficparo,"\n");          eip +=eij[i][j][(int)age];
     }          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
          }
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;        fprintf(ficreseij,"%9.4f", eip );
       }
   p=param[1][1];      fprintf(ficreseij,"\n");
        
   /* Reads comments: lines beginning with '#' */    }
   while((c=getc(ficpar))=='#' && c!= EOF){    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     ungetc(c,ficpar);    printf("\n");
     fgets(line, MAXLINE, ficpar);    fprintf(ficlog,"\n");
     puts(line);    
     fputs(line,ficparo);  }
   }  
   ungetc(c,ficpar);  void cvevsij(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[] )
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  {
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    /* Covariances of health expectancies eij and of total life expectancies according
   for(i=1; i <=nlstate; i++){     to initial status i, ei. .
     for(j=1; j <=nlstate+ndeath-1; j++){    */
       fscanf(ficpar,"%1d%1d",&i1,&j1);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
       printf("%1d%1d",i,j);    int nhstepma, nstepma; /* Decreasing with age */
       fprintf(ficparo,"%1d%1d",i1,j1);    double age, agelim, hf;
       for(k=1; k<=ncovmodel;k++){    double ***p3matp, ***p3matm, ***varhe;
         fscanf(ficpar,"%le",&delti3[i][j][k]);    double **dnewm,**doldm;
         printf(" %le",delti3[i][j][k]);    double *xp, *xm;
         fprintf(ficparo," %le",delti3[i][j][k]);    double **gp, **gm;
       }    double ***gradg, ***trgradg;
       fscanf(ficpar,"\n");    int theta;
       printf("\n");  
       fprintf(ficparo,"\n");    double eip, vip;
     }  
   }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   delti=delti3[1][1];    xp=vector(1,npar);
      xm=vector(1,npar);
   /* Reads comments: lines beginning with '#' */    dnewm=matrix(1,nlstate*nlstate,1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    pstamp(ficresstdeij);
     puts(line);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fputs(line,ficparo);    fprintf(ficresstdeij,"# Age");
   }    for(i=1; i<=nlstate;i++){
   ungetc(c,ficpar);      for(j=1; j<=nlstate;j++)
          fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   matcov=matrix(1,npar,1,npar);      fprintf(ficresstdeij," e%1d. ",i);
   for(i=1; i <=npar; i++){    }
     fscanf(ficpar,"%s",&str);    fprintf(ficresstdeij,"\n");
     printf("%s",str);  
     fprintf(ficparo,"%s",str);    pstamp(ficrescveij);
     for(j=1; j <=i; j++){    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
       fscanf(ficpar," %le",&matcov[i][j]);    fprintf(ficrescveij,"# Age");
       printf(" %.5le",matcov[i][j]);    for(i=1; i<=nlstate;i++)
       fprintf(ficparo," %.5le",matcov[i][j]);      for(j=1; j<=nlstate;j++){
     }        cptj= (j-1)*nlstate+i;
     fscanf(ficpar,"\n");        for(i2=1; i2<=nlstate;i2++)
     printf("\n");          for(j2=1; j2<=nlstate;j2++){
     fprintf(ficparo,"\n");            cptj2= (j2-1)*nlstate+i2;
   }            if(cptj2 <= cptj)
   for(i=1; i <=npar; i++)              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
     for(j=i+1;j<=npar;j++)          }
       matcov[i][j]=matcov[j][i];      }
        fprintf(ficrescveij,"\n");
   printf("\n");    
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     /*-------- Rewriting paramater file ----------*/    }
      strcpy(rfileres,"r");    /* "Rparameterfile */    else  hstepm=estepm;   
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    /* We compute the life expectancy from trapezoids spaced every estepm months
      strcat(rfileres,".");    /* */     * This is mainly to measure the difference between two models: for example
      strcat(rfileres,optionfilext);    /* Other files have txt extension */     * if stepm=24 months pijx are given only every 2 years and by summing them
     if((ficres =fopen(rfileres,"w"))==NULL) {     * we are calculating an estimate of the Life Expectancy assuming a linear 
       printf("Problem writing new parameter file: %s\n", fileres);goto end;     * progression in between and thus overestimating or underestimating according
     }     * to the curvature of the survival function. If, for the same date, we 
     fprintf(ficres,"#%s\n",version);     * 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 
     /*-------- data file ----------*/     * hypothesis. A more precise result, taking into account a more precise
     if((fic=fopen(datafile,"r"))==NULL)    {     * curvature will be obtained if estepm is as small as stepm. */
       printf("Problem with datafile: %s\n", datafile);goto end;  
     }    /* 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. 
     n= lastobs;       nhstepm is the number of hstepm from age to agelim 
     severity = vector(1,maxwav);       nstepm is the number of stepm from age to agelin. 
     outcome=imatrix(1,maxwav+1,1,n);       Look at hpijx to understand the reason of that which relies in memory size
     num=ivector(1,n);       and note for a fixed period like estepm months */
     moisnais=vector(1,n);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     annais=vector(1,n);       survival function given by stepm (the optimization length). Unfortunately it
     moisdc=vector(1,n);       means that if the survival funtion is printed only each two years of age and if
     andc=vector(1,n);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     agedc=vector(1,n);       results. So we changed our mind and took the option of the best precision.
     cod=ivector(1,n);    */
     weight=vector(1,n);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */  
     mint=matrix(1,maxwav,1,n);    /* If stepm=6 months */
     anint=matrix(1,maxwav,1,n);    /* nhstepm age range expressed in number of stepm */
     s=imatrix(1,maxwav+1,1,n);    agelim=AGESUP;
     adl=imatrix(1,maxwav+1,1,n);        nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     tab=ivector(1,NCOVMAX);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     ncodemax=ivector(1,8);    /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     i=1;    
     while (fgets(line, MAXLINE, fic) != NULL)    {    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       if ((i >= firstobs) && (i <=lastobs)) {    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
         for (j=maxwav;j>=1;j--){    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    gp=matrix(0,nhstepm,1,nlstate*nlstate);
           strcpy(line,stra);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
           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 (age=bage; age<=fage; age ++){ 
         }      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
              /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      /* if (stepm >= YEARM) hstepm=1;*/
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      /* If stepm=6 months */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
          in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      
         for (j=ncovcol;j>=1;j--){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }      /* Computing  Variances of health expectancies */
         num[i]=atol(stra);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
                 decrease memory allocation */
         /*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;}*/        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         i=i+1;          xm[i] = x[i] - (i==theta ?delti[theta]:0);
       }        }
     }        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
     /* printf("ii=%d", ij);        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
        scanf("%d",i);*/    
   imx=i-1; /* Number of individuals */        for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
   /* for (i=1; i<=imx; i++){            for(h=0; h<=nhstepm-1; h++){
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
     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;        for(ij=1; ij<= nlstate*nlstate; ij++)
      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(h=0; h<=nhstepm-1; h++){
   */            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
            }
   /* Calculation of the number of parameter from char model*/      }/* End theta */
   Tvar=ivector(1,15);      
   Tprod=ivector(1,15);      
   Tvaraff=ivector(1,15);      for(h=0; h<=nhstepm-1; h++)
   Tvard=imatrix(1,15,1,2);        for(j=1; j<=nlstate*nlstate;j++)
   Tage=ivector(1,15);                for(theta=1; theta <=npar; theta++)
                trgradg[h][j][theta]=gradg[h][theta][j];
   if (strlen(model) >1){      
     j=0, j1=0, k1=1, k2=1;  
     j=nbocc(model,'+');       for(ij=1;ij<=nlstate*nlstate;ij++)
     j1=nbocc(model,'*');        for(ji=1;ji<=nlstate*nlstate;ji++)
     cptcovn=j+1;          varhe[ij][ji][(int)age] =0.;
     cptcovprod=j1;  
           printf("%d|",(int)age);fflush(stdout);
     strcpy(modelsav,model);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){       for(h=0;h<=nhstepm-1;h++){
       printf("Error. Non available option model=%s ",model);        for(k=0;k<=nhstepm-1;k++){
       goto end;          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     }          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
              for(ij=1;ij<=nlstate*nlstate;ij++)
     for(i=(j+1); i>=1;i--){            for(ji=1;ji<=nlstate*nlstate;ji++)
       cutv(stra,strb,modelsav,'+');              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        }
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      }
       /*scanf("%d",i);*/  
       if (strchr(strb,'*')) {      /* Computing expectancies */
         cutv(strd,strc,strb,'*');      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
         if (strcmp(strc,"age")==0) {      for(i=1; i<=nlstate;i++)
           cptcovprod--;        for(j=1; j<=nlstate;j++)
           cutv(strb,stre,strd,'V');          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           Tvar[i]=atoi(stre);            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
           cptcovage++;            
             Tage[cptcovage]=i;            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
             /*printf("stre=%s ", stre);*/  
         }          }
         else if (strcmp(strd,"age")==0) {  
           cptcovprod--;      fprintf(ficresstdeij,"%3.0f",age );
           cutv(strb,stre,strc,'V');      for(i=1; i<=nlstate;i++){
           Tvar[i]=atoi(stre);        eip=0.;
           cptcovage++;        vip=0.;
           Tage[cptcovage]=i;        for(j=1; j<=nlstate;j++){
         }          eip += eij[i][j][(int)age];
         else {          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
           cutv(strb,stre,strc,'V');            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           Tvar[i]=ncovcol+k1;          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
           cutv(strb,strc,strd,'V');        }
           Tprod[k1]=i;        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
           Tvard[k1][1]=atoi(strc);      }
           Tvard[k1][2]=atoi(stre);      fprintf(ficresstdeij,"\n");
           Tvar[cptcovn+k2]=Tvard[k1][1];  
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      fprintf(ficrescveij,"%3.0f",age );
           for (k=1; k<=lastobs;k++)      for(i=1; i<=nlstate;i++)
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        for(j=1; j<=nlstate;j++){
           k1++;          cptj= (j-1)*nlstate+i;
           k2=k2+2;          for(i2=1; i2<=nlstate;i2++)
         }            for(j2=1; j2<=nlstate;j2++){
       }              cptj2= (j2-1)*nlstate+i2;
       else {              if(cptj2 <= cptj)
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
        /*  scanf("%d",i);*/            }
       cutv(strd,strc,strb,'V');        }
       Tvar[i]=atoi(strc);      fprintf(ficrescveij,"\n");
       }     
       strcpy(modelsav,stra);      }
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
         scanf("%d",i);*/    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     }    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
 }    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
      free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("cptcovprod=%d ", cptcovprod);    printf("\n");
   scanf("%d ",i);*/    fprintf(ficlog,"\n");
     fclose(fic);  
     free_vector(xm,1,npar);
     /*  if(mle==1){*/    free_vector(xp,1,npar);
     if (weightopt != 1) { /* Maximisation without weights*/    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
       for(i=1;i<=n;i++) weight[i]=1.0;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     /*-calculation of age at interview from date of interview and age at death -*/  }
     agev=matrix(1,maxwav,1,imx);  
   /************ Variance ******************/
     for (i=1; i<=imx; i++) {  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[])
       for(m=2; (m<= maxwav); m++) {  {
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    /* Variance of health expectancies */
          anint[m][i]=9999;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
          s[m][i]=-1;    /* double **newm;*/
        }    double **dnewm,**doldm;
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    double **dnewmp,**doldmp;
       }    int i, j, nhstepm, hstepm, h, nstepm ;
     }    int k, cptcode;
     double *xp;
     for (i=1; i<=imx; i++)  {    double **gp, **gm;  /* for var eij */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    double ***gradg, ***trgradg; /*for var eij */
       for(m=1; (m<= maxwav); m++){    double **gradgp, **trgradgp; /* for var p point j */
         if(s[m][i] >0){    double *gpp, *gmp; /* for var p point j */
           if (s[m][i] >= nlstate+1) {    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
             if(agedc[i]>0)    double ***p3mat;
               if(moisdc[i]!=99 && andc[i]!=9999)    double age,agelim, hf;
                 agev[m][i]=agedc[i];    double ***mobaverage;
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    int theta;
            else {    char digit[4];
               if (andc[i]!=9999){    char digitp[25];
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;    char fileresprobmorprev[FILENAMELENGTH];
               }  
             }    if(popbased==1){
           }      if(mobilav!=0)
           else if(s[m][i] !=9){ /* Should no more exist */        strcpy(digitp,"-populbased-mobilav-");
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      else strcpy(digitp,"-populbased-nomobil-");
             if(mint[m][i]==99 || anint[m][i]==9999)    }
               agev[m][i]=1;    else 
             else if(agev[m][i] <agemin){      strcpy(digitp,"-stablbased-");
               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);*/    if (mobilav!=0) {
             }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             else if(agev[m][i] >agemax){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
               agemax=agev[m][i];        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
             }      }
             /*agev[m][i]=anint[m][i]-annais[i];*/    }
             /*   agev[m][i] = age[i]+2*m;*/  
           }    strcpy(fileresprobmorprev,"prmorprev"); 
           else { /* =9 */    sprintf(digit,"%-d",ij);
             agev[m][i]=1;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
             s[m][i]=-1;    strcat(fileresprobmorprev,digit); /* Tvar to be done */
           }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         }    strcat(fileresprobmorprev,fileres);
         else /*= 0 Unknown */    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
           agev[m][i]=1;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
        }
     }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     for (i=1; i<=imx; i++)  {   
       for(m=1; (m<= maxwav); m++){    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
         if (s[m][i] > (nlstate+ndeath)) {    pstamp(ficresprobmorprev);
           printf("Error: Wrong value in nlstate or ndeath\n");      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);
           goto end;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
         }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       }      fprintf(ficresprobmorprev," p.%-d SE",j);
     }      for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    }  
     fprintf(ficresprobmorprev,"\n");
     free_vector(severity,1,maxwav);    fprintf(ficgp,"\n# Routine varevsij");
     free_imatrix(outcome,1,maxwav+1,1,n);    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     free_vector(moisnais,1,n);    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");
     free_vector(annais,1,n);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     /* free_matrix(mint,1,maxwav,1,n);  /*   } */
        free_matrix(anint,1,maxwav,1,n);*/    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_vector(moisdc,1,n);    pstamp(ficresvij);
     free_vector(andc,1,n);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
          fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
     wav=ivector(1,imx);    else
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    fprintf(ficresvij,"# Age");
        for(i=1; i<=nlstate;i++)
     /* Concatenates waves */      for(j=1; j<=nlstate;j++)
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
       Tcode=ivector(1,100);    xp=vector(1,npar);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    dnewm=matrix(1,nlstate,1,npar);
       ncodemax[1]=1;    doldm=matrix(1,nlstate,1,nlstate);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
          doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    codtab=imatrix(1,100,1,10);  
    h=0;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
    m=pow(2,cptcoveff);    gpp=vector(nlstate+1,nlstate+ndeath);
      gmp=vector(nlstate+1,nlstate+ndeath);
    for(k=1;k<=cptcoveff; k++){    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      for(i=1; i <=(m/pow(2,k));i++){    
        for(j=1; j <= ncodemax[k]; j++){    if(estepm < stepm){
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      printf ("Problem %d lower than %d\n",estepm, stepm);
            h++;    }
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    else  hstepm=estepm;   
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    /* 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. 
        }       nhstepm is the number of hstepm from age to agelim 
      }       nstepm is the number of stepm from age to agelin. 
    }       Look at function hpijx to understand why (it is linked to memory size questions) */
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       codtab[1][2]=1;codtab[2][2]=2; */       survival function given by stepm (the optimization length). Unfortunately it
    /* for(i=1; i <=m ;i++){       means that if the survival funtion is printed every two years of age and if
       for(k=1; k <=cptcovn; k++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);       results. So we changed our mind and took the option of the best precision.
       }    */
       printf("\n");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       }    agelim = AGESUP;
       scanf("%d",i);*/    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
          nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
    /* Calculates basic frequencies. Computes observed prevalence at single age      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
        and prints on file fileres'p'. */      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
          gp=matrix(0,nhstepm,1,nlstate);
          gm=matrix(0,nhstepm,1,nlstate);
     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 */      for(theta=1; theta <=npar; theta++){
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
              }
     /* For Powell, parameters are in a vector p[] starting at p[1]        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  
         if (popbased==1) {
     if(mle==1){          if(mobilav ==0){
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);            for(i=1; i<=nlstate;i++)
     }              prlim[i][i]=probs[(int)age][i][ij];
              }else{ /* mobilav */ 
     /*--------- results files --------------*/            for(i=1; i<=nlstate;i++)
     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);              prlim[i][i]=mobaverage[(int)age][i][ij];
            }
         }
    jk=1;    
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        for(j=1; j<= nlstate; j++){
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          for(h=0; h<=nhstepm; h++){
    for(i=1,jk=1; i <=nlstate; i++){            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
      for(k=1; k <=(nlstate+ndeath); k++){              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
        if (k != i)          }
          {        }
            printf("%d%d ",i,k);        /* This for computing probability of death (h=1 means
            fprintf(ficres,"%1d%1d ",i,k);           computed over hstepm matrices product = hstepm*stepm months) 
            for(j=1; j <=ncovmodel; j++){           as a weighted average of prlim.
              printf("%f ",p[jk]);        */
              fprintf(ficres,"%f ",p[jk]);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
              jk++;          for(i=1,gpp[j]=0.; i<= nlstate; i++)
            }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
            printf("\n");        }    
            fprintf(ficres,"\n");        /* end probability of death */
          }  
      }        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
    }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
  if(mle==1){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     /* Computing hessian and covariance matrix */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     ftolhess=ftol; /* Usually correct */   
     hesscov(matcov, p, npar, delti, ftolhess, func);        if (popbased==1) {
  }          if(mobilav ==0){
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");            for(i=1; i<=nlstate;i++)
     printf("# Scales (for hessian or gradient estimation)\n");              prlim[i][i]=probs[(int)age][i][ij];
      for(i=1,jk=1; i <=nlstate; i++){          }else{ /* mobilav */ 
       for(j=1; j <=nlstate+ndeath; j++){            for(i=1; i<=nlstate;i++)
         if (j!=i) {              prlim[i][i]=mobaverage[(int)age][i][ij];
           fprintf(ficres,"%1d%1d",i,j);          }
           printf("%1d%1d",i,j);        }
           for(k=1; k<=ncovmodel;k++){  
             printf(" %.5e",delti[jk]);        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
             fprintf(ficres," %.5e",delti[jk]);          for(h=0; h<=nhstepm; h++){
             jk++;            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
           }              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           printf("\n");          }
           fprintf(ficres,"\n");        }
         }        /* This for computing probability of death (h=1 means
       }           computed over hstepm matrices product = hstepm*stepm months) 
      }           as a weighted average of prlim.
            */
     k=1;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     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");          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     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");           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     for(i=1;i<=npar;i++){        }    
       /*  if (k>nlstate) k=1;        /* end probability of death */
       i1=(i-1)/(ncovmodel*nlstate)+1;  
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        for(j=1; j<= nlstate; j++) /* vareij */
       printf("%s%d%d",alph[k],i1,tab[i]);*/          for(h=0; h<=nhstepm; h++){
       fprintf(ficres,"%3d",i);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       printf("%3d",i);          }
       for(j=1; j<=i;j++){  
         fprintf(ficres," %.5e",matcov[i][j]);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
         printf(" %.5e",matcov[i][j]);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       }        }
       fprintf(ficres,"\n");  
       printf("\n");      } /* End theta */
       k++;  
     }      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
      
     while((c=getc(ficpar))=='#' && c!= EOF){      for(h=0; h<=nhstepm; h++) /* veij */
       ungetc(c,ficpar);        for(j=1; j<=nlstate;j++)
       fgets(line, MAXLINE, ficpar);          for(theta=1; theta <=npar; theta++)
       puts(line);            trgradg[h][j][theta]=gradg[h][theta][j];
       fputs(line,ficparo);  
     }      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     ungetc(c,ficpar);        for(theta=1; theta <=npar; theta++)
            trgradgp[j][theta]=gradgp[theta][j];
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&ageminpar,&agemaxpar, &bage, &fage);    
      
     if (fage <= 2) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       bage = ageminpar;      for(i=1;i<=nlstate;i++)
       fage = agemaxpar;        for(j=1;j<=nlstate;j++)
     }          vareij[i][j][(int)age] =0.;
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      for(h=0;h<=nhstepm;h++){
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",ageminpar,agemaxpar,bage,fage);        for(k=0;k<=nhstepm;k++){
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",ageminpar,agemaxpar,bage,fage);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
     while((c=getc(ficpar))=='#' && c!= EOF){          for(i=1;i<=nlstate;i++)
     ungetc(c,ficpar);            for(j=1;j<=nlstate;j++)
     fgets(line, MAXLINE, ficpar);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     puts(line);        }
     fputs(line,ficparo);      }
   }    
   ungetc(c,ficpar);      /* pptj */
        matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
                varppt[j][i]=doldmp[j][i];
   while((c=getc(ficpar))=='#' && c!= EOF){      /* end ppptj */
     ungetc(c,ficpar);      /*  x centered again */
     fgets(line, MAXLINE, ficpar);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     puts(line);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     fputs(line,ficparo);   
   }      if (popbased==1) {
   ungetc(c,ficpar);        if(mobilav ==0){
            for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        }else{ /* mobilav */ 
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
   fscanf(ficpar,"pop_based=%d\n",&popbased);        }
   fprintf(ficparo,"pop_based=%d\n",popbased);        }
   fprintf(ficres,"pop_based=%d\n",popbased);                 
        /* This for computing probability of death (h=1 means
   while((c=getc(ficpar))=='#' && c!= EOF){         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     ungetc(c,ficpar);         as a weighted average of prlim.
     fgets(line, MAXLINE, ficpar);      */
     puts(line);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
     fputs(line,ficparo);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   }          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   ungetc(c,ficpar);      }    
       /* end probability of death */
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);  
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
 while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);      } 
     puts(line);      fprintf(ficresprobmorprev,"\n");
     fputs(line,ficparo);  
   }      fprintf(ficresvij,"%.0f ",age );
   ungetc(c,ficpar);      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        }
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
 /*------------ gnuplot -------------*/      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      } /* End age */
 /*------------ free_vector  -------------*/    free_vector(gpp,nlstate+1,nlstate+ndeath);
  chdir(path);    free_vector(gmp,nlstate+1,nlstate+ndeath);
      free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
  free_ivector(wav,1,imx);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
  free_ivector(num,1,n);    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
  free_vector(agedc,1,n);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
  /*free_matrix(covar,1,NCOVMAX,1,n);*/  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
  fclose(ficparo);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
  fclose(ficres);    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));
 /*--------- index.htm --------*/    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));
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(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);
    */
   /*--------------- Prevalence limit --------------*/  /*   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);
   strcpy(filerespl,"pl");  
   strcat(filerespl,fileres);    free_vector(xp,1,npar);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    free_matrix(doldm,1,nlstate,1,nlstate);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    free_matrix(dnewm,1,nlstate,1,npar);
   }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   fprintf(ficrespl,"#Prevalence limit\n");    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   fprintf(ficrespl,"#Age ");    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    fclose(ficresprobmorprev);
   fprintf(ficrespl,"\n");    fflush(ficgp);
      fflush(fichtm); 
   prlim=matrix(1,nlstate,1,nlstate);  }  /* end varevsij */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /************ Variance of prevlim ******************/
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  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[])
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  {
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    /* Variance of prevalence limit */
   k=0;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   agebase=ageminpar;    double **newm;
   agelim=agemaxpar;    double **dnewm,**doldm;
   ftolpl=1.e-10;    int i, j, nhstepm, hstepm;
   i1=cptcoveff;    int k, cptcode;
   if (cptcovn < 1){i1=1;}    double *xp;
     double *gp, *gm;
   for(cptcov=1;cptcov<=i1;cptcov++){    double **gradg, **trgradg;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double age,agelim;
         k=k+1;    int theta;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    
         fprintf(ficrespl,"\n#******");    pstamp(ficresvpl);
         for(j=1;j<=cptcoveff;j++)    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresvpl,"# Age");
         fprintf(ficrespl,"******\n");    for(i=1; i<=nlstate;i++)
                fprintf(ficresvpl," %1d-%1d",i,i);
         for (age=agebase; age<=agelim; age++){    fprintf(ficresvpl,"\n");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
           fprintf(ficrespl,"%.0f",age );    xp=vector(1,npar);
           for(i=1; i<=nlstate;i++)    dnewm=matrix(1,nlstate,1,npar);
           fprintf(ficrespl," %.5f", prlim[i][i]);    doldm=matrix(1,nlstate,1,nlstate);
           fprintf(ficrespl,"\n");    
         }    hstepm=1*YEARM; /* Every year of age */
       }    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     }    agelim = AGESUP;
   fclose(ficrespl);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   /*------------- h Pij x at various ages ------------*/      if (stepm >= YEARM) hstepm=1;
        nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      gradg=matrix(1,npar,1,nlstate);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      gp=vector(1,nlstate);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      gm=vector(1,nlstate);
   }  
   printf("Computing pij: result on file '%s' \n", filerespij);      for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ /* Computes gradient */
   stepsize=(int) (stepm+YEARM-1)/YEARM;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   /*if (stepm<=24) stepsize=2;*/        }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   agelim=AGESUP;        for(i=1;i<=nlstate;i++)
   hstepm=stepsize*YEARM; /* Every year of age */          gp[i] = prlim[i][i];
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      
          for(i=1; i<=npar; i++) /* Computes gradient */
   k=0;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   for(cptcov=1;cptcov<=i1;cptcov++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(i=1;i<=nlstate;i++)
       k=k+1;          gm[i] = prlim[i][i];
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)        for(i=1;i<=nlstate;i++)
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         fprintf(ficrespij,"******\n");      } /* End theta */
          
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      trgradg =matrix(1,nlstate,1,npar);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      for(j=1; j<=nlstate;j++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(theta=1; theta <=npar; theta++)
           oldm=oldms;savm=savms;          trgradg[j][theta]=gradg[theta][j];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");      for(i=1;i<=nlstate;i++)
           for(i=1; i<=nlstate;i++)        varpl[i][(int)age] =0.;
             for(j=1; j<=nlstate+ndeath;j++)      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
               fprintf(ficrespij," %1d-%1d",i,j);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
           fprintf(ficrespij,"\n");      for(i=1;i<=nlstate;i++)
           for (h=0; h<=nhstepm; h++){        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)      fprintf(ficresvpl,"%.0f ",age );
               for(j=1; j<=nlstate+ndeath;j++)      for(i=1; i<=nlstate;i++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
             fprintf(ficrespij,"\n");      fprintf(ficresvpl,"\n");
           }      free_vector(gp,1,nlstate);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      free_vector(gm,1,nlstate);
           fprintf(ficrespij,"\n");      free_matrix(gradg,1,npar,1,nlstate);
         }      free_matrix(trgradg,1,nlstate,1,npar);
     }    } /* End age */
   }  
     free_vector(xp,1,npar);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   fclose(ficrespij);  
   }
   
   /*---------- Forecasting ------------------*/  /************ Variance of one-step probabilities  ******************/
   if((stepm == 1) && (strcmp(model,".")==0)){  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[])
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);  {
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    int i, j=0,  i1, k1, l1, t, tj;
     free_matrix(mint,1,maxwav,1,n);    int k2, l2, j1,  z1;
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    int k=0,l, cptcode;
     free_vector(weight,1,n);}    int first=1, first1;
   else{    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     erreur=108;    double **dnewm,**doldm;
     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);    double *xp;
   }    double *gp, *gm;
      double **gradg, **trgradg;
     double **mu;
   /*---------- Health expectancies and variances ------------*/    double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   strcpy(filerest,"t");    int theta;
   strcat(filerest,fileres);    char fileresprob[FILENAMELENGTH];
   if((ficrest=fopen(filerest,"w"))==NULL) {    char fileresprobcov[FILENAMELENGTH];
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    char fileresprobcor[FILENAMELENGTH];
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    double ***varpij;
   
     strcpy(fileresprob,"prob"); 
   strcpy(filerese,"e");    strcat(fileresprob,fileres);
   strcat(filerese,fileres);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   if((ficreseij=fopen(filerese,"w"))==NULL) {      printf("Problem with resultfile: %s\n", fileresprob);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   }    }
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
  strcpy(fileresv,"v");    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   strcat(fileresv,fileres);      printf("Problem with resultfile: %s\n", fileresprobcov);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    }
   }    strcpy(fileresprobcor,"probcor"); 
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   k=0;      printf("Problem with resultfile: %s\n", fileresprobcor);
   for(cptcov=1;cptcov<=i1;cptcov++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    }
       k=k+1;    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       fprintf(ficrest,"\n#****** ");    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       for(j=1;j<=cptcoveff;j++)    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       fprintf(ficrest,"******\n");    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       fprintf(ficreseij,"\n#****** ");    pstamp(ficresprob);
       for(j=1;j<=cptcoveff;j++)    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresprob,"# Age");
       fprintf(ficreseij,"******\n");    pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
       fprintf(ficresvij,"\n#****** ");    fprintf(ficresprobcov,"# Age");
       for(j=1;j<=cptcoveff;j++)    pstamp(ficresprobcor);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
       fprintf(ficresvij,"******\n");    fprintf(ficresprobcor,"# Age");
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;    for(i=1; i<=nlstate;i++)
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);        for(j=1; j<=(nlstate+ndeath);j++){
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
       oldm=oldms;savm=savms;        fprintf(ficresprobcov," p%1d-%1d ",i,j);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
          }  
    /* fprintf(ficresprob,"\n");
      fprintf(ficresprobcov,"\n");
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    fprintf(ficresprobcor,"\n");
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);   */
       fprintf(ficrest,"\n");    xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       epj=vector(1,nlstate+1);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       for(age=bage; age <=fage ;age++){    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
         if (popbased==1) {    first=1;
           for(i=1; i<=nlstate;i++)    fprintf(ficgp,"\n# Routine varprob");
             prlim[i][i]=probs[(int)age][i][k];    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
         }    fprintf(fichtm,"\n");
          
         fprintf(ficrest," %4.0f",age);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    file %s<br>\n",optionfilehtmcov);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    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.\
           epj[nlstate+1] +=epj[j];   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. \
         for(i=1, vepp=0.;i <=nlstate;i++)  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
           for(j=1;j <=nlstate;j++)  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
             vepp += vareij[i][j][(int)age];  standard deviations wide on each axis. <br>\
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
         for(j=1;j <=nlstate;j++){   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
         }  
         fprintf(ficrest,"\n");    cov[1]=1;
       }    tj=cptcoveff;
     }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   }    j1=0;
     for(t=1; t<=tj;t++){
   fclose(ficreseij);      for(i1=1; i1<=ncodemax[t];i1++){ 
   fclose(ficresvij);        j1++;
   fclose(ficrest);        if  (cptcovn>0) {
   fclose(ficpar);          fprintf(ficresprob, "\n#********** Variable "); 
   free_vector(epj,1,nlstate+1);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresprob, "**********\n#\n");
   /*------- Variance limit prevalence------*/            fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   strcpy(fileresvpl,"vpl");          fprintf(ficresprobcov, "**********\n#\n");
   strcat(fileresvpl,fileres);          
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          fprintf(ficgp, "\n#********** Variable "); 
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     exit(0);          fprintf(ficgp, "**********\n#\n");
   }          
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   k=0;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          
       k=k+1;          fprintf(ficresprobcor, "\n#********** Variable ");    
       fprintf(ficresvpl,"\n#****** ");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       for(j=1;j<=cptcoveff;j++)          fprintf(ficresprobcor, "**********\n#");    
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }
       fprintf(ficresvpl,"******\n");        
              for (age=bage; age<=fage; age ++){ 
       varpl=matrix(1,nlstate,(int) bage, (int) fage);          cov[2]=age;
       oldm=oldms;savm=savms;          for (k=1; k<=cptcovn;k++) {
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     }          }
  }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
   fclose(ficresvpl);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
   /*---------- End : free ----------------*/          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
            gp=vector(1,(nlstate)*(nlstate+ndeath));
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          gm=vector(1,(nlstate)*(nlstate+ndeath));
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      
            for(theta=1; theta <=npar; theta++){
              for(i=1; i<=npar; i++)
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);            
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);            
              k=0;
   free_matrix(matcov,1,npar,1,npar);            for(i=1; i<= (nlstate); i++){
   free_vector(delti,1,npar);              for(j=1; j<=(nlstate+ndeath);j++){
   free_matrix(agev,1,maxwav,1,imx);                k=k+1;
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                gp[k]=pmmij[i][j];
               }
   if(erreur >0)            }
     printf("End of Imach with error or warning %d\n",erreur);            
   else   printf("End of Imach\n");            for(i=1; i<=npar; i++)
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
        
   /* 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);*/            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   /*printf("Total time was %d uSec.\n", total_usecs);*/            k=0;
   /*------ End -----------*/            for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
  end:                gm[k]=pmmij[i][j];
 #ifdef windows              }
   /* chdir(pathcd);*/            }
 #endif       
  /*system("wgnuplot graph.plt");*/            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
  /*system("../gp37mgw/wgnuplot graph.plt");*/              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
  /*system("cd ../gp37mgw");*/          }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  
  strcpy(plotcmd,GNUPLOTPROGRAM);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
  strcat(plotcmd," ");            for(theta=1; theta <=npar; theta++)
  strcat(plotcmd,optionfilegnuplot);              trgradg[j][theta]=gradg[theta][j];
  system(plotcmd);          
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
 #ifdef windows          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   while (z[0] != 'q') {          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     /* chdir(path); */          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     scanf("%s",z);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') system(optionfilehtm);          pmij(pmmij,cov,ncovmodel,x,nlstate);
     else if (z[0] == 'g') system(plotcmd);          
     else if (z[0] == 'q') exit(0);          k=0;
   }          for(i=1; i<=(nlstate); i++){
 #endif            for(j=1; j<=(nlstate+ndeath);j++){
 }              k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           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);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       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);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       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));
                     }/* if first */
                   } /* age mod 5 */
                 } /* 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;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      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 ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        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\
    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> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           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> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\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>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> 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",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (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",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"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 ++) {
          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;
     int vpopbased=0;
   
     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*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     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);
       goto end;
       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 \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\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++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       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); /* s[i][j] health state for wave i and individual j */ 
     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,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           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 '%s' at line number %ld 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);
             fprintf(ficlog,"Error reading data around '%s' at line number %ld 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);fflush(ficlog);
             goto end;
           }
         }
         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 for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           goto end;
         }
         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 for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           goto end;
       }
       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);
         fprintf(ficlog,"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);fflush(ficlog);
           goto end;
       }
       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);
         fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         goto end;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             goto end;
           }
         }
         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);
           fprintf(ficlog,"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);fflush(ficlog);
           goto end;
         }
         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,NCOVMAX); /* Was 15 changed to NCOVMAX. 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; /* Number of covariates V1+V2+V3 =>2+1=3 */
       cptcovprod=j1; /*Number of products  V1*V2 =1 */
       
       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);fflush(ficlog);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 
                                        stra=V2
                                       */ 
         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 V1+V3*age+V2 strb=V3*age*/
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre);  /* V1+V3*age+V2 Tvar[2]=3 */
             cptcovage++; /* Sum the number of covariates including ages as a product */
             Tage[cptcovage]=i;  /* Tage[1] =2 */
             /*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 V1+V3*V2+V2  strb=V3*V2*/
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[i]=ncovcol+k1;  /* find 'n' in Vn and stores in Tvar. 
                                     If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;  /* Tprod[1]  */
             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);  /* modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 */ 
         /*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 */
   
     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++){ /* scans any effective covariate */
       for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             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 codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][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,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><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",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><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",\
             optionfilehtm,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 */
       globpr=1;/* debug */
       /*    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("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",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;
           /* to clean */
           printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
           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); */
         /*      } */
       }
     
   
       /* 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);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       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);
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         }
       }
       fclose(ficreseij);
   
   
       /*---------- 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(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);
   
       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(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;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(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;
           cvevsij(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);
           pstamp(ficrest);
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms;
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# 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 (vpopbased==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(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 */
    endfree:
     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_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>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     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.1.35  
changed lines
  Added in v.1.131


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