Diff for /imach/src/imach.c between versions 1.30 and 1.136

version 1.30, 2002/03/08 16:17:18 version 1.136, 2010/04/26 20:30:53
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.136  2010/04/26 20:30:53  brouard
      (Module): merging some libgsl code. Fixing computation
   This program computes Healthy Life Expectancies from    of likelione (using inter/intrapolation if mle = 0) in order to
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    get same likelihood as if mle=1.
   first survey ("cross") where individuals from different ages are    Some cleaning of code and comments added.
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.135  2009/10/29 15:33:14  brouard
   second wave of interviews ("longitudinal") which measure each change    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.134  2009/10/29 13:18:53  brouard
   model. More health states you consider, more time is necessary to reach the    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.133  2009/07/06 10:21:25  brouard
   probabibility to be observed in state j at the second wave    just nforces
   conditional to be observed in state i at the first wave. Therefore  
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Revision 1.132  2009/07/06 08:22:05  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    Many tings
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.131  2009/06/20 16:22:47  brouard
   you to do it.  More covariates you add, slower the    Some dimensions resccaled
   convergence.  
     Revision 1.130  2009/05/26 06:44:34  brouard
   The advantage of this computer programme, compared to a simple    (Module): Max Covariate is now set to 20 instead of 8. A
   multinomial logistic model, is clear when the delay between waves is not    lot of cleaning with variables initialized to 0. Trying to make
   identical for each individual. Also, if a individual missed an    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.129  2007/08/31 13:49:27  lievre
     Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    Revision 1.128  2006/06/30 13:02:05  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    (Module): Clarifications on computing e.j
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.127  2006/04/28 18:11:50  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    (Module): Yes the sum of survivors was wrong since
   and the contribution of each individual to the likelihood is simply    imach-114 because nhstepm was no more computed in the age
   hPijx.    loop. Now we define nhstepma in the age loop.
     (Module): In order to speed up (in case of numerous covariates) we
   Also this programme outputs the covariance matrix of the parameters but also    compute health expectancies (without variances) in a first step
   of the life expectancies. It also computes the prevalence limits.    and then all the health expectancies with variances or standard
      deviation (needs data from the Hessian matrices) which slows the
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    computation.
            Institut national d'études démographiques, Paris.    In the future we should be able to stop the program is only health
   This software have been partly granted by Euro-REVES, a concerted action    expectancies and graph are needed without standard deviations.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.126  2006/04/28 17:23:28  brouard
   software can be distributed freely for non commercial use. Latest version    (Module): Yes the sum of survivors was wrong since
   can be accessed at http://euroreves.ined.fr/imach .    imach-114 because nhstepm was no more computed in the age
   **********************************************************************/    loop. Now we define nhstepma in the age loop.
      Version 0.98h
 #include <math.h>  
 #include <stdio.h>    Revision 1.125  2006/04/04 15:20:31  lievre
 #include <stdlib.h>    Errors in calculation of health expectancies. Age was not initialized.
 #include <unistd.h>    Forecasting file added.
   
 #define MAXLINE 256    Revision 1.124  2006/03/22 17:13:53  lievre
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    Parameters are printed with %lf instead of %f (more numbers after the comma).
 #define FILENAMELENGTH 80    The log-likelihood is printed in the log file
 /*#define DEBUG*/  
 #define windows    Revision 1.123  2006/03/20 10:52:43  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    * imach.c (Module): <title> changed, corresponds to .htm file
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    name. <head> headers where missing.
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    * imach.c (Module): Weights can have a decimal point as for
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
 #define NINTERVMAX 8    Modification of warning when the covariates values are not 0 or
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    1.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Version 0.98g
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.122  2006/03/20 09:45:41  brouard
 #define YEARM 12. /* Number of months per year */    (Module): Weights can have a decimal point as for
 #define AGESUP 130    English (a comma might work with a correct LC_NUMERIC environment,
 #define AGEBASE 40    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
     1.
 int erreur; /* Error number */    Version 0.98g
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.121  2006/03/16 17:45:01  lievre
 int npar=NPARMAX;    * imach.c (Module): Comments concerning covariates added
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    * imach.c (Module): refinements in the computation of lli if
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    status=-2 in order to have more reliable computation if stepm is
 int popbased=0;    not 1 month. Version 0.98f
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.120  2006/03/16 15:10:38  lievre
 int maxwav; /* Maxim number of waves */    (Module): refinements in the computation of lli if
 int jmin, jmax; /* min, max spacing between 2 waves */    status=-2 in order to have more reliable computation if stepm is
 int mle, weightopt;    not 1 month. Version 0.98f
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Revision 1.119  2006/03/15 17:42:26  brouard
 double jmean; /* Mean space between 2 waves */    (Module): Bug if status = -2, the loglikelihood was
 double **oldm, **newm, **savm; /* Working pointers to matrices */    computed as likelihood omitting the logarithm. Version O.98e
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Revision 1.118  2006/03/14 18:20:07  brouard
 FILE *ficgp,*ficresprob,*ficpop;    (Module): varevsij Comments added explaining the second
 FILE *ficreseij;    table of variances if popbased=1 .
   char filerese[FILENAMELENGTH];    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
  FILE  *ficresvij;    (Module): Function pstamp added
   char fileresv[FILENAMELENGTH];    (Module): Version 0.98d
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Revision 1.117  2006/03/14 17:16:22  brouard
     (Module): varevsij Comments added explaining the second
 #define NR_END 1    table of variances if popbased=1 .
 #define FREE_ARG char*    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #define FTOL 1.0e-10    (Module): Function pstamp added
     (Module): Version 0.98d
 #define NRANSI  
 #define ITMAX 200    Revision 1.116  2006/03/06 10:29:27  brouard
     (Module): Variance-covariance wrong links and
 #define TOL 2.0e-4    varian-covariance of ej. is needed (Saito).
   
 #define CGOLD 0.3819660    Revision 1.115  2006/02/27 12:17:45  brouard
 #define ZEPS 1.0e-10    (Module): One freematrix added in mlikeli! 0.98c
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.114  2006/02/26 12:57:58  brouard
 #define GOLD 1.618034    (Module): Some improvements in processing parameter
 #define GLIMIT 100.0    filename with strsep.
 #define TINY 1.0e-20  
     Revision 1.113  2006/02/24 14:20:24  brouard
 static double maxarg1,maxarg2;    (Module): Memory leaks checks with valgrind and:
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    datafile was not closed, some imatrix were not freed and on matrix
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    allocation too.
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.112  2006/01/30 09:55:26  brouard
 #define rint(a) floor(a+0.5)    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   
 static double sqrarg;    Revision 1.111  2006/01/25 20:38:18  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    (Module): Lots of cleaning and bugs added (Gompertz)
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    (Module): Comments can be added in data file. Missing date values
     can be a simple dot '.'.
 int imx;  
 int stepm;    Revision 1.110  2006/01/25 00:51:50  brouard
 /* Stepm, step in month: minimum step interpolation*/    (Module): Lots of cleaning and bugs added (Gompertz)
   
 int m,nb;    Revision 1.109  2006/01/24 19:37:15  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    (Module): Comments (lines starting with a #) are allowed in data.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Revision 1.108  2006/01/19 18:05:42  lievre
 double dateintmean=0;    Gnuplot problem appeared...
     To be fixed
 double *weight;  
 int **s; /* Status */    Revision 1.107  2006/01/19 16:20:37  brouard
 double *agedc, **covar, idx;    Test existence of gnuplot in imach path
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.106  2006/01/19 13:24:36  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Some cleaning and links added in html output
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.105  2006/01/05 20:23:19  lievre
 /**************** split *************************/    *** empty log message ***
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Revision 1.104  2005/09/30 16:11:43  lievre
    char *s;                             /* pointer */    (Module): sump fixed, loop imx fixed, and simplifications.
    int  l1, l2;                         /* length counters */    (Module): If the status is missing at the last wave but we know
     that the person is alive, then we can code his/her status as -2
    l1 = strlen( path );                 /* length of path */    (instead of missing=-1 in earlier versions) and his/her
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    contributions to the likelihood is 1 - Prob of dying from last
 #ifdef windows    health status (= 1-p13= p11+p12 in the easiest case of somebody in
    s = strrchr( path, '\\' );           /* find last / */    the healthy state at last known wave). Version is 0.98
 #else  
    s = strrchr( path, '/' );            /* find last / */    Revision 1.103  2005/09/30 15:54:49  lievre
 #endif    (Module): sump fixed, loop imx fixed, and simplifications.
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    Revision 1.102  2004/09/15 17:31:30  brouard
       extern char       *getwd( );    Add the possibility to read data file including tab characters.
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.101  2004/09/15 10:38:38  brouard
 #else    Fix on curr_time
       extern char       *getcwd( );  
     Revision 1.100  2004/07/12 18:29:06  brouard
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Add version for Mac OS X. Just define UNIX in Makefile
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.99  2004/06/05 08:57:40  brouard
       }    *** empty log message ***
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.98  2004/05/16 15:05:56  brouard
       s++;                              /* after this, the filename */    New version 0.97 . First attempt to estimate force of mortality
       l2 = strlen( s );                 /* length of filename */    directly from the data i.e. without the need of knowing the health
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    state at each age, but using a Gompertz model: log u =a + b*age .
       strcpy( name, s );                /* save file name */    This is the basic analysis of mortality and should be done before any
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    other analysis, in order to test if the mortality estimated from the
       dirc[l1-l2] = 0;                  /* add zero */    cross-longitudinal survey is different from the mortality estimated
    }    from other sources like vital statistic data.
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows    The same imach parameter file can be used but the option for mle should be -3.
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else    Agnès, who wrote this part of the code, tried to keep most of the
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    former routines in order to include the new code within the former code.
 #endif  
    s = strrchr( name, '.' );            /* find last / */    The output is very simple: only an estimate of the intercept and of
    s++;    the slope with 95% confident intervals.
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);    Current limitations:
    l2= strlen( s)+1;    A) Even if you enter covariates, i.e. with the
    strncpy( finame, name, l1-l2);    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
    finame[l1-l2]= 0;    B) There is no computation of Life Expectancy nor Life Table.
    return( 0 );                         /* we're done */  
 }    Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
 /******************************************/  
     Revision 1.96  2003/07/15 15:38:55  brouard
 void replace(char *s, char*t)    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 {    rewritten within the same printf. Workaround: many printfs.
   int i;  
   int lg=20;    Revision 1.95  2003/07/08 07:54:34  brouard
   i=0;    * imach.c (Repository):
   lg=strlen(t);    (Repository): Using imachwizard code to output a more meaningful covariance
   for(i=0; i<= lg; i++) {    matrix (cov(a12,c31) instead of numbers.
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Revision 1.94  2003/06/27 13:00:02  brouard
   }    Just cleaning
 }  
     Revision 1.93  2003/06/25 16:33:55  brouard
 int nbocc(char *s, char occ)    (Module): On windows (cygwin) function asctime_r doesn't
 {    exist so I changed back to asctime which exists.
   int i,j=0;    (Module): Version 0.96b
   int lg=20;  
   i=0;    Revision 1.92  2003/06/25 16:30:45  brouard
   lg=strlen(s);    (Module): On windows (cygwin) function asctime_r doesn't
   for(i=0; i<= lg; i++) {    exist so I changed back to asctime which exists.
   if  (s[i] == occ ) j++;  
   }    Revision 1.91  2003/06/25 15:30:29  brouard
   return j;    * imach.c (Repository): Duplicated warning errors corrected.
 }    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
 void cutv(char *u,char *v, char*t, char occ)    is stamped in powell.  We created a new html file for the graphs
 {    concerning matrix of covariance. It has extension -cov.htm.
   int i,lg,j,p=0;  
   i=0;    Revision 1.90  2003/06/24 12:34:15  brouard
   for(j=0; j<=strlen(t)-1; j++) {    (Module): Some bugs corrected for windows. Also, when
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    mle=-1 a template is output in file "or"mypar.txt with the design
   }    of the covariance matrix to be input.
   
   lg=strlen(t);    Revision 1.89  2003/06/24 12:30:52  brouard
   for(j=0; j<p; j++) {    (Module): Some bugs corrected for windows. Also, when
     (u[j] = t[j]);    mle=-1 a template is output in file "or"mypar.txt with the design
   }    of the covariance matrix to be input.
      u[p]='\0';  
     Revision 1.88  2003/06/23 17:54:56  brouard
    for(j=0; j<= lg; 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.
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }    Revision 1.87  2003/06/18 12:26:01  brouard
 }    Version 0.96
   
 /********************** nrerror ********************/    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
 void nrerror(char error_text[])    routine fileappend.
 {  
   fprintf(stderr,"ERREUR ...\n");    Revision 1.85  2003/06/17 13:12:43  brouard
   fprintf(stderr,"%s\n",error_text);    * imach.c (Repository): Check when date of death was earlier that
   exit(1);    current date of interview. It may happen when the death was just
 }    prior to the death. In this case, dh was negative and likelihood
 /*********************** vector *******************/    was wrong (infinity). We still send an "Error" but patch by
 double *vector(int nl, int nh)    assuming that the date of death was just one stepm after the
 {    interview.
   double *v;    (Repository): Because some people have very long ID (first column)
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    we changed int to long in num[] and we added a new lvector for
   if (!v) nrerror("allocation failure in vector");    memory allocation. But we also truncated to 8 characters (left
   return v-nl+NR_END;    truncation)
 }    (Repository): No more line truncation errors.
   
 /************************ free vector ******************/    Revision 1.84  2003/06/13 21:44:43  brouard
 void free_vector(double*v, int nl, int nh)    * imach.c (Repository): Replace "freqsummary" at a correct
 {    place. It differs from routine "prevalence" which may be called
   free((FREE_ARG)(v+nl-NR_END));    many times. Probs is memory consuming and must be used with
 }    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    Revision 1.83  2003/06/10 13:39:11  lievre
 {    *** empty log message ***
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    Revision 1.82  2003/06/05 15:57:20  brouard
   if (!v) nrerror("allocation failure in ivector");    Add log in  imach.c and  fullversion number is now printed.
   return v-nl+NR_END;  
 }  */
   /*
 /******************free ivector **************************/     Interpolated Markov Chain
 void free_ivector(int *v, long nl, long nh)  
 {    Short summary of the programme:
   free((FREE_ARG)(v+nl-NR_END));    
 }    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 /******************* imatrix *******************************/    first survey ("cross") where individuals from different ages are
 int **imatrix(long nrl, long nrh, long ncl, long nch)    interviewed on their health status or degree of disability (in the
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    case of a health survey which is our main interest) -2- at least a
 {    second wave of interviews ("longitudinal") which measure each change
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    (if any) in individual health status.  Health expectancies are
   int **m;    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
   /* allocate pointers to rows */    Maximum Likelihood of the parameters involved in the model.  The
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    simplest model is the multinomial logistic model where pij is the
   if (!m) nrerror("allocation failure 1 in matrix()");    probability to be observed in state j at the second wave
   m += NR_END;    conditional to be observed in state i at the first wave. Therefore
   m -= nrl;    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
      complex model than "constant and age", you should modify the program
   /* allocate rows and set pointers to them */    where the markup *Covariates have to be included here again* invites
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    you to do it.  More covariates you add, slower the
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    convergence.
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    The advantage of this computer programme, compared to a simple
      multinomial logistic model, is clear when the delay between waves is not
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    identical for each individual. Also, if a individual missed an
      intermediate interview, the information is lost, but taken into
   /* return pointer to array of pointers to rows */    account using an interpolation or extrapolation.  
   return 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
 /****************** free_imatrix *************************/    split into an exact number (nh*stepm) of unobserved intermediate
 void free_imatrix(m,nrl,nrh,ncl,nch)    states. This elementary transition (by month, quarter,
       int **m;    semester or year) is modelled as a multinomial logistic.  The hPx
       long nch,ncl,nrh,nrl;    matrix is simply the matrix product of nh*stepm elementary matrices
      /* free an int matrix allocated by imatrix() */    and the contribution of each individual to the likelihood is simply
 {    hPijx.
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));    Also this programme outputs the covariance matrix of the parameters but also
 }    of the life expectancies. It also computes the period (stable) prevalence. 
     
 /******************* matrix *******************************/    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 double **matrix(long nrl, long nrh, long ncl, long nch)             Institut national d'études démographiques, Paris.
 {    This software have been partly granted by Euro-REVES, a concerted action
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    from the European Union.
   double **m;    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    can be accessed at http://euroreves.ined.fr/imach .
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   m -= nrl;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    **********************************************************************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /*
   m[nrl] += NR_END;    main
   m[nrl] -= ncl;    read parameterfile
     read datafile
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    concatwav
   return m;    freqsummary
 }    if (mle >= 1)
       mlikeli
 /*************************free matrix ************************/    print results files
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    if mle==1 
 {       computes hessian
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    read end of parameter file: agemin, agemax, bage, fage, estepm
   free((FREE_ARG)(m+nrl-NR_END));        begin-prev-date,...
 }    open gnuplot file
     open html file
 /******************* ma3x *******************************/    period (stable) prevalence
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)     for age prevalim()
 {    h Pij x
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    variance of p varprob
   double ***m;    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Variance-covariance of DFLE
   if (!m) nrerror("allocation failure 1 in matrix()");    prevalence()
   m += NR_END;     movingaverage()
   m -= nrl;    varevsij() 
     if popbased==1 varevsij(,popbased)
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    total life expectancies
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Variance of period (stable) prevalence
   m[nrl] += NR_END;   end
   m[nrl] -= ncl;  */
   
   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()");  #include <math.h>
   m[nrl][ncl] += NR_END;  #include <stdio.h>
   m[nrl][ncl] -= nll;  #include <stdlib.h>
   for (j=ncl+1; j<=nch; j++)  #include <string.h>
     m[nrl][j]=m[nrl][j-1]+nlay;  #include <unistd.h>
    
   for (i=nrl+1; i<=nrh; i++) {  #include <limits.h>
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #include <sys/types.h>
     for (j=ncl+1; j<=nch; j++)  #include <sys/stat.h>
       m[i][j]=m[i][j-1]+nlay;  #include <errno.h>
   }  extern int errno;
   return m;  
 }  /* #include <sys/time.h> */
   #include <time.h>
 /*************************free ma3x ************************/  #include "timeval.h"
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {  #ifdef GSL
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #include <gsl/gsl_errno.h>
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #include <gsl/gsl_multimin.h>
   free((FREE_ARG)(m+nrl-NR_END));  #endif
 }  
   /* #include <libintl.h> */
 /***************** f1dim *************************/  /* #define _(String) gettext (String) */
 extern int ncom;  
 extern double *pcom,*xicom;  #define MAXLINE 256
 extern double (*nrfunc)(double []);  
    #define GNUPLOTPROGRAM "gnuplot"
 double f1dim(double x)  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 {  #define FILENAMELENGTH 132
   int j;  
   double f;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   double *xt;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
    
   xt=vector(1,ncom);  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  #define NINTERVMAX 8
   return f;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 }  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 20 /* Maximum number of covariates */
 /*****************brent *************************/  #define MAXN 20000
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #define YEARM 12. /* Number of months per year */
 {  #define AGESUP 130
   int iter;  #define AGEBASE 40
   double a,b,d,etemp;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   double fu,fv,fw,fx;  #ifdef UNIX
   double ftemp;  #define DIRSEPARATOR '/'
   double p,q,r,tol1,tol2,u,v,w,x,xm;  #define CHARSEPARATOR "/"
   double e=0.0;  #define ODIRSEPARATOR '\\'
    #else
   a=(ax < cx ? ax : cx);  #define DIRSEPARATOR '\\'
   b=(ax > cx ? ax : cx);  #define CHARSEPARATOR "\\"
   x=w=v=bx;  #define ODIRSEPARATOR '/'
   fw=fv=fx=(*f)(x);  #endif
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);  /* $Id$ */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  /* $State$ */
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  char version[]="Imach version 0.98m, April 2010, INED-EUROREVES-Institut de longevite ";
 #ifdef DEBUG  char fullversion[]="$Revision$ $Date$"; 
     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);  char strstart[80];
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 #endif  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  int nvar=0, nforce=0; /* Number of variables, number of forces */
       *xmin=x;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
       return fx;  int npar=NPARMAX;
     }  int nlstate=2; /* Number of live states */
     ftemp=fu;  int ndeath=1; /* Number of dead states */
     if (fabs(e) > tol1) {  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       r=(x-w)*(fx-fv);  int popbased=0;
       q=(x-v)*(fx-fw);  
       p=(x-v)*q-(x-w)*r;  int *wav; /* Number of waves for this individuual 0 is possible */
       q=2.0*(q-r);  int maxwav=0; /* Maxim number of waves */
       if (q > 0.0) p = -p;  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
       q=fabs(q);  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
       etemp=e;  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
       e=d;                     to the likelihood and the sum of weights (done by funcone)*/
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  int mle=1, weightopt=0;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       else {  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
         d=p/q;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
         u=x+d;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
         if (u-a < tol2 || b-u < tol2)  double jmean=1; /* Mean space between 2 waves */
           d=SIGN(tol1,xm-x);  double **oldm, **newm, **savm; /* Working pointers to matrices */
       }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     } else {  /*FILE *fic ; */ /* Used in readdata only */
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
     }  FILE *ficlog, *ficrespow;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  int globpr=0; /* Global variable for printing or not */
     fu=(*f)(u);  double fretone; /* Only one call to likelihood */
     if (fu <= fx) {  long ipmx=0; /* Number of contributions */
       if (u >= x) a=x; else b=x;  double sw; /* Sum of weights */
       SHFT(v,w,x,u)  char filerespow[FILENAMELENGTH];
         SHFT(fv,fw,fx,fu)  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
         } else {  FILE *ficresilk;
           if (u < x) a=u; else b=u;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
           if (fu <= fw || w == x) {  FILE *ficresprobmorprev;
             v=w;  FILE *fichtm, *fichtmcov; /* Html File */
             w=u;  FILE *ficreseij;
             fv=fw;  char filerese[FILENAMELENGTH];
             fw=fu;  FILE *ficresstdeij;
           } else if (fu <= fv || v == x || v == w) {  char fileresstde[FILENAMELENGTH];
             v=u;  FILE *ficrescveij;
             fv=fu;  char filerescve[FILENAMELENGTH];
           }  FILE  *ficresvij;
         }  char fileresv[FILENAMELENGTH];
   }  FILE  *ficresvpl;
   nrerror("Too many iterations in brent");  char fileresvpl[FILENAMELENGTH];
   *xmin=x;  char title[MAXLINE];
   return fx;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 }  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 /****************** mnbrak ***********************/  char command[FILENAMELENGTH];
   int  outcmd=0;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 {  
   double ulim,u,r,q, dum;  char filelog[FILENAMELENGTH]; /* Log file */
   double fu;  char filerest[FILENAMELENGTH];
    char fileregp[FILENAMELENGTH];
   *fa=(*func)(*ax);  char popfile[FILENAMELENGTH];
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
       }  struct timezone tzp;
   *cx=(*bx)+GOLD*(*bx-*ax);  extern int gettimeofday();
   *fc=(*func)(*cx);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   while (*fb > *fc) {  long time_value;
     r=(*bx-*ax)*(*fb-*fc);  extern long time();
     q=(*bx-*cx)*(*fb-*fa);  char strcurr[80], strfor[80];
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  char *endptr;
     ulim=(*bx)+GLIMIT*(*cx-*bx);  long lval;
     if ((*bx-u)*(u-*cx) > 0.0) {  double dval;
       fu=(*func)(u);  
     } else if ((*cx-u)*(u-ulim) > 0.0) {  #define NR_END 1
       fu=(*func)(u);  #define FREE_ARG char*
       if (fu < *fc) {  #define FTOL 1.0e-10
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  #define NRANSI 
           }  #define ITMAX 200 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  #define TOL 2.0e-4 
       fu=(*func)(u);  
     } else {  #define CGOLD 0.3819660 
       u=(*cx)+GOLD*(*cx-*bx);  #define ZEPS 1.0e-10 
       fu=(*func)(u);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     }  
     SHFT(*ax,*bx,*cx,u)  #define GOLD 1.618034 
       SHFT(*fa,*fb,*fc,fu)  #define GLIMIT 100.0 
       }  #define TINY 1.0e-20 
 }  
   static double maxarg1,maxarg2;
 /*************** linmin ************************/  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 int ncom;    
 double *pcom,*xicom;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 double (*nrfunc)(double []);  #define rint(a) floor(a+0.5)
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  static double sqrarg;
 {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   double brent(double ax, double bx, double cx,  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
                double (*f)(double), double tol, double *xmin);  int agegomp= AGEGOMP;
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  int imx; 
               double *fc, double (*func)(double));  int stepm=1;
   int j;  /* Stepm, step in month: minimum step interpolation*/
   double xx,xmin,bx,ax;  
   double fx,fb,fa;  int estepm;
    /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   ncom=n;  
   pcom=vector(1,n);  int m,nb;
   xicom=vector(1,n);  long *num;
   nrfunc=func;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   for (j=1;j<=n;j++) {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     pcom[j]=p[j];  double **pmmij, ***probs;
     xicom[j]=xi[j];  double *ageexmed,*agecens;
   }  double dateintmean=0;
   ax=0.0;  
   xx=1.0;  double *weight;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  int **s; /* Status */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  double *agedc, **covar, idx;
 #ifdef DEBUG  int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  double *lsurv, *lpop, *tpop;
 #endif  
   for (j=1;j<=n;j++) {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
     xi[j] *= xmin;  double ftolhess; /* Tolerance for computing hessian */
     p[j] += xi[j];  
   }  /**************** split *************************/
   free_vector(xicom,1,n);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   free_vector(pcom,1,n);  {
 }    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
        the name of the file (name), its extension only (ext) and its first part of the name (finame)
 /*************** powell ************************/    */ 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    char  *ss;                            /* pointer */
             double (*func)(double []))    int   l1, l2;                         /* length counters */
 {  
   void linmin(double p[], double xi[], int n, double *fret,    l1 = strlen(path );                   /* length of path */
               double (*func)(double []));    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   int i,ibig,j;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   double del,t,*pt,*ptt,*xit;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   double fp,fptt;      strcpy( name, path );               /* we got the fullname name because no directory */
   double *xits;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   pt=vector(1,n);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   ptt=vector(1,n);      /* get current working directory */
   xit=vector(1,n);      /*    extern  char* getcwd ( char *buf , int len);*/
   xits=vector(1,n);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   *fret=(*func)(p);        return( GLOCK_ERROR_GETCWD );
   for (j=1;j<=n;j++) pt[j]=p[j];      }
   for (*iter=1;;++(*iter)) {      /* got dirc from getcwd*/
     fp=(*fret);      printf(" DIRC = %s \n",dirc);
     ibig=0;    } else {                              /* strip direcotry from path */
     del=0.0;      ss++;                               /* after this, the filename */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      l2 = strlen( ss );                  /* length of filename */
     for (i=1;i<=n;i++)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       printf(" %d %.12f",i, p[i]);      strcpy( name, ss );         /* save file name */
     printf("\n");      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     for (i=1;i<=n;i++) {      dirc[l1-l2] = 0;                    /* add zero */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      printf(" DIRC2 = %s \n",dirc);
       fptt=(*fret);    }
 #ifdef DEBUG    /* We add a separator at the end of dirc if not exists */
       printf("fret=%lf \n",*fret);    l1 = strlen( dirc );                  /* length of directory */
 #endif    if( dirc[l1-1] != DIRSEPARATOR ){
       printf("%d",i);fflush(stdout);      dirc[l1] =  DIRSEPARATOR;
       linmin(p,xit,n,fret,func);      dirc[l1+1] = 0; 
       if (fabs(fptt-(*fret)) > del) {      printf(" DIRC3 = %s \n",dirc);
         del=fabs(fptt-(*fret));    }
         ibig=i;    ss = strrchr( name, '.' );            /* find last / */
       }    if (ss >0){
 #ifdef DEBUG      ss++;
       printf("%d %.12e",i,(*fret));      strcpy(ext,ss);                     /* save extension */
       for (j=1;j<=n;j++) {      l1= strlen( name);
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      l2= strlen(ss)+1;
         printf(" x(%d)=%.12e",j,xit[j]);      strncpy( finame, name, l1-l2);
       }      finame[l1-l2]= 0;
       for(j=1;j<=n;j++)    }
         printf(" p=%.12e",p[j]);  
       printf("\n");    return( 0 );                          /* we're done */
 #endif  }
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  
 #ifdef DEBUG  /******************************************/
       int k[2],l;  
       k[0]=1;  void replace_back_to_slash(char *s, char*t)
       k[1]=-1;  {
       printf("Max: %.12e",(*func)(p));    int i;
       for (j=1;j<=n;j++)    int lg=0;
         printf(" %.12e",p[j]);    i=0;
       printf("\n");    lg=strlen(t);
       for(l=0;l<=1;l++) {    for(i=0; i<= lg; i++) {
         for (j=1;j<=n;j++) {      (s[i] = t[i]);
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      if (t[i]== '\\') s[i]='/';
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    }
         }  }
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  char *trimbb(char *out, char *in)
 #endif  { /* Trim multiple blanks in line */
     char *s;
     s=out;
       free_vector(xit,1,n);    while (*in != '\0'){
       free_vector(xits,1,n);      while( *in == ' ' && *(in+1) == ' ' && *(in+1) != '\0'){
       free_vector(ptt,1,n);        in++;
       free_vector(pt,1,n);      }
       return;      *out++ = *in++;
     }    }
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    *out='\0';
     for (j=1;j<=n;j++) {    return s;
       ptt[j]=2.0*p[j]-pt[j];  }
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];  int nbocc(char *s, char occ)
     }  {
     fptt=(*func)(ptt);    int i,j=0;
     if (fptt < fp) {    int lg=20;
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    i=0;
       if (t < 0.0) {    lg=strlen(s);
         linmin(p,xit,n,fret,func);    for(i=0; i<= lg; i++) {
         for (j=1;j<=n;j++) {    if  (s[i] == occ ) j++;
           xi[j][ibig]=xi[j][n];    }
           xi[j][n]=xit[j];    return j;
         }  }
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  void cutv(char *u,char *v, char*t, char occ)
         for(j=1;j<=n;j++)  {
           printf(" %.12e",xit[j]);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
         printf("\n");       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
 #endif       gives u="abcedf" and v="ghi2j" */
       }    int i,lg,j,p=0;
     }    i=0;
   }    for(j=0; j<=strlen(t)-1; j++) {
 }      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     }
 /**** Prevalence limit ****************/  
     lg=strlen(t);
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    for(j=0; j<p; j++) {
 {      (u[j] = t[j]);
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    }
      matrix by transitions matrix until convergence is reached */       u[p]='\0';
   
   int i, ii,j,k;     for(j=0; j<= lg; j++) {
   double min, max, maxmin, maxmax,sumnew=0.;      if (j>=(p+1))(v[j-p-1] = t[j]);
   double **matprod2();    }
   double **out, cov[NCOVMAX], **pmij();  }
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */  /********************** nrerror ********************/
   
   for (ii=1;ii<=nlstate+ndeath;ii++)  void nrerror(char error_text[])
     for (j=1;j<=nlstate+ndeath;j++){  {
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    fprintf(stderr,"ERREUR ...\n");
     }    fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
    cov[1]=1.;  }
    /*********************** vector *******************/
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  double *vector(int nl, int nh)
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  {
     newm=savm;    double *v;
     /* Covariates have to be included here again */    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
      cov[2]=agefin;    if (!v) nrerror("allocation failure in vector");
      return v-nl+NR_END;
       for (k=1; k<=cptcovn;k++) {  }
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  /************************ free vector ******************/
       }  void free_vector(double*v, int nl, int nh)
       for (k=1; k<=cptcovage;k++)  {
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    free((FREE_ARG)(v+nl-NR_END));
       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]]];  
   /************************ivector *******************************/
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  int *ivector(long nl,long nh)
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  {
     int *v;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     if (!v) nrerror("allocation failure in ivector");
     savm=oldm;    return v-nl+NR_END;
     oldm=newm;  }
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){  /******************free ivector **************************/
       min=1.;  void free_ivector(int *v, long nl, long nh)
       max=0.;  {
       for(i=1; i<=nlstate; i++) {    free((FREE_ARG)(v+nl-NR_END));
         sumnew=0;  }
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  /************************lvector *******************************/
         max=FMAX(max,prlim[i][j]);  long *lvector(long nl,long nh)
         min=FMIN(min,prlim[i][j]);  {
       }    long *v;
       maxmin=max-min;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       maxmax=FMAX(maxmax,maxmin);    if (!v) nrerror("allocation failure in ivector");
     }    return v-nl+NR_END;
     if(maxmax < ftolpl){  }
       return prlim;  
     }  /******************free lvector **************************/
   }  void free_lvector(long *v, long nl, long nh)
 }  {
     free((FREE_ARG)(v+nl-NR_END));
 /*************** transition probabilities ***************/  }
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  /******************* imatrix *******************************/
 {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   double s1, s2;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   /*double t34;*/  { 
   int i,j,j1, nc, ii, jj;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     int **m; 
     for(i=1; i<= nlstate; i++){    
     for(j=1; j<i;j++){    /* allocate pointers to rows */ 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         /*s2 += param[i][j][nc]*cov[nc];*/    if (!m) nrerror("allocation failure 1 in matrix()"); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    m += NR_END; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    m -= nrl; 
       }    
       ps[i][j]=s2;    
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    /* allocate rows and set pointers to them */ 
     }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     for(j=i+1; j<=nlstate+ndeath;j++){    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    m[nrl] += NR_END; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    m[nrl] -= ncl; 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    
       }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       ps[i][j]=s2;    
     }    /* return pointer to array of pointers to rows */ 
   }    return m; 
     /*ps[3][2]=1;*/  } 
   
   for(i=1; i<= nlstate; i++){  /****************** free_imatrix *************************/
      s1=0;  void free_imatrix(m,nrl,nrh,ncl,nch)
     for(j=1; j<i; j++)        int **m;
       s1+=exp(ps[i][j]);        long nch,ncl,nrh,nrl; 
     for(j=i+1; j<=nlstate+ndeath; j++)       /* free an int matrix allocated by imatrix() */ 
       s1+=exp(ps[i][j]);  { 
     ps[i][i]=1./(s1+1.);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     for(j=1; j<i; j++)    free((FREE_ARG) (m+nrl-NR_END)); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];  } 
     for(j=i+1; j<=nlstate+ndeath; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /******************* matrix *******************************/
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  double **matrix(long nrl, long nrh, long ncl, long nch)
   } /* end i */  {
     long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    double **m;
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       ps[ii][ii]=1;    if (!m) nrerror("allocation failure 1 in matrix()");
     }    m += NR_END;
   }    m -= nrl;
   
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     for(jj=1; jj<= nlstate+ndeath; jj++){    m[nrl] += NR_END;
      printf("%lf ",ps[ii][jj]);    m[nrl] -= ncl;
    }  
     printf("\n ");    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     }    return m;
     printf("\n ");printf("%lf ",cov[2]);*/    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
 /*     */
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  }
   goto end;*/  
     return ps;  /*************************free matrix ************************/
 }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
 /**************** Product of 2 matrices ******************/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  }
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  /******************* ma3x *******************************/
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   /* in, b, out are matrice of pointers which should have been initialized  {
      before: only the contents of out is modified. The function returns    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
      a pointer to pointers identical to out */    double ***m;
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     for(k=ncolol; k<=ncoloh; k++)    if (!m) nrerror("allocation failure 1 in matrix()");
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    m += NR_END;
         out[i][k] +=in[i][j]*b[j][k];    m -= nrl;
   
   return out;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
     m[nrl] -= ncl;
 /************* Higher Matrix Product ***************/  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
      duration (i.e. until    m[nrl][ncl] += NR_END;
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    m[nrl][ncl] -= nll;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    for (j=ncl+1; j<=nch; j++) 
      (typically every 2 years instead of every month which is too big).      m[nrl][j]=m[nrl][j-1]+nlay;
      Model is determined by parameters x and covariates have to be    
      included manually here.    for (i=nrl+1; i<=nrh; i++) {
       m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
      */      for (j=ncl+1; j<=nch; j++) 
         m[i][j]=m[i][j-1]+nlay;
   int i, j, d, h, k;    }
   double **out, cov[NCOVMAX];    return m; 
   double **newm;    /*  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)
   /* Hstepm could be zero and should return the unit matrix */    */
   for (i=1;i<=nlstate+ndeath;i++)  }
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);  /*************************free ma3x ************************/
       po[i][j][0]=(i==j ? 1.0 : 0.0);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     }  {
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   for(h=1; h <=nhstepm; h++){    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     for(d=1; d <=hstepm; d++){    free((FREE_ARG)(m+nrl-NR_END));
       newm=savm;  }
       /* Covariates have to be included here again */  
       cov[1]=1.;  /*************** function subdirf ***********/
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  char *subdirf(char fileres[])
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  {
       for (k=1; k<=cptcovage;k++)    /* Caution optionfilefiname is hidden */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    strcpy(tmpout,optionfilefiname);
       for (k=1; k<=cptcovprod;k++)    strcat(tmpout,"/"); /* Add to the right */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    strcat(tmpout,fileres);
     return tmpout;
   }
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  /*************** function subdirf2 ***********/
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  char *subdirf2(char fileres[], char *preop)
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  {
       savm=oldm;    
       oldm=newm;    /* Caution optionfilefiname is hidden */
     }    strcpy(tmpout,optionfilefiname);
     for(i=1; i<=nlstate+ndeath; i++)    strcat(tmpout,"/");
       for(j=1;j<=nlstate+ndeath;j++) {    strcat(tmpout,preop);
         po[i][j][h]=newm[i][j];    strcat(tmpout,fileres);
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    return tmpout;
          */  }
       }  
   } /* end h */  /*************** function subdirf3 ***********/
   return po;  char *subdirf3(char fileres[], char *preop, char *preop2)
 }  {
     
     /* Caution optionfilefiname is hidden */
 /*************** log-likelihood *************/    strcpy(tmpout,optionfilefiname);
 double func( double *x)    strcat(tmpout,"/");
 {    strcat(tmpout,preop);
   int i, ii, j, k, mi, d, kk;    strcat(tmpout,preop2);
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    strcat(tmpout,fileres);
   double **out;    return tmpout;
   double sw; /* Sum of weights */  }
   double lli; /* Individual log likelihood */  
   long ipmx;  /***************** f1dim *************************/
   /*extern weight */  extern int ncom; 
   /* We are differentiating ll according to initial status */  extern double *pcom,*xicom;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  extern double (*nrfunc)(double []); 
   /*for(i=1;i<imx;i++)   
     printf(" %d\n",s[4][i]);  double f1dim(double x) 
   */  { 
   cov[1]=1.;    int j; 
     double f;
   for(k=1; k<=nlstate; k++) ll[k]=0.;    double *xt; 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){   
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    xt=vector(1,ncom); 
     for(mi=1; mi<= wav[i]-1; mi++){    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       for (ii=1;ii<=nlstate+ndeath;ii++)    f=(*nrfunc)(xt); 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    free_vector(xt,1,ncom); 
       for(d=0; d<dh[mi][i]; d++){    return f; 
         newm=savm;  } 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
         for (kk=1; kk<=cptcovage;kk++) {  /*****************brent *************************/
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
         }  { 
            int iter; 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    double a,b,d,etemp;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    double fu,fv,fw,fx;
         savm=oldm;    double ftemp;
         oldm=newm;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
            double e=0.0; 
           
       } /* end mult */    a=(ax < cx ? ax : cx); 
          b=(ax > cx ? ax : cx); 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    x=w=v=bx; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    fw=fv=fx=(*f)(x); 
       ipmx +=1;    for (iter=1;iter<=ITMAX;iter++) { 
       sw += weight[i];      xm=0.5*(a+b); 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     } /* end of wave */      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   } /* end of individual */      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  #ifdef DEBUG
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      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);
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      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);
   return -l;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 }  #endif
       if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         *xmin=x; 
 /*********** Maximum Likelihood Estimation ***************/        return fx; 
       } 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      ftemp=fu;
 {      if (fabs(e) > tol1) { 
   int i,j, iter;        r=(x-w)*(fx-fv); 
   double **xi,*delti;        q=(x-v)*(fx-fw); 
   double fret;        p=(x-v)*q-(x-w)*r; 
   xi=matrix(1,npar,1,npar);        q=2.0*(q-r); 
   for (i=1;i<=npar;i++)        if (q > 0.0) p = -p; 
     for (j=1;j<=npar;j++)        q=fabs(q); 
       xi[i][j]=(i==j ? 1.0 : 0.0);        etemp=e; 
   printf("Powell\n");        e=d; 
   powell(p,xi,npar,ftol,&iter,&fret,func);        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)); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        else { 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));          d=p/q; 
           u=x+d; 
 }          if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
 /**** Computes Hessian and covariance matrix ***/        } 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      } else { 
 {        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double  **a,**y,*x,pd;      } 
   double **hess;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   int i, j,jk;      fu=(*f)(u); 
   int *indx;      if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
   double hessii(double p[], double delta, int theta, double delti[]);        SHFT(v,w,x,u) 
   double hessij(double p[], double delti[], int i, int j);          SHFT(fv,fw,fx,fu) 
   void lubksb(double **a, int npar, int *indx, double b[]) ;          } else { 
   void ludcmp(double **a, int npar, int *indx, double *d) ;            if (u < x) a=u; else b=u; 
             if (fu <= fw || w == x) { 
   hess=matrix(1,npar,1,npar);              v=w; 
               w=u; 
   printf("\nCalculation of the hessian matrix. Wait...\n");              fv=fw; 
   for (i=1;i<=npar;i++){              fw=fu; 
     printf("%d",i);fflush(stdout);            } else if (fu <= fv || v == x || v == w) { 
     hess[i][i]=hessii(p,ftolhess,i,delti);              v=u; 
     /*printf(" %f ",p[i]);*/              fv=fu; 
     /*printf(" %lf ",hess[i][i]);*/            } 
   }          } 
      } 
   for (i=1;i<=npar;i++) {    nrerror("Too many iterations in brent"); 
     for (j=1;j<=npar;j++)  {    *xmin=x; 
       if (j>i) {    return fx; 
         printf(".%d%d",i,j);fflush(stdout);  } 
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];      /****************** mnbrak ***********************/
         /*printf(" %lf ",hess[i][j]);*/  
       }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     }              double (*func)(double)) 
   }  { 
   printf("\n");    double ulim,u,r,q, dum;
     double fu; 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");   
      *fa=(*func)(*ax); 
   a=matrix(1,npar,1,npar);    *fb=(*func)(*bx); 
   y=matrix(1,npar,1,npar);    if (*fb > *fa) { 
   x=vector(1,npar);      SHFT(dum,*ax,*bx,dum) 
   indx=ivector(1,npar);        SHFT(dum,*fb,*fa,dum) 
   for (i=1;i<=npar;i++)        } 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    *cx=(*bx)+GOLD*(*bx-*ax); 
   ludcmp(a,npar,indx,&pd);    *fc=(*func)(*cx); 
     while (*fb > *fc) { 
   for (j=1;j<=npar;j++) {      r=(*bx-*ax)*(*fb-*fc); 
     for (i=1;i<=npar;i++) x[i]=0;      q=(*bx-*cx)*(*fb-*fa); 
     x[j]=1;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     lubksb(a,npar,indx,x);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     for (i=1;i<=npar;i++){      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       matcov[i][j]=x[i];      if ((*bx-u)*(u-*cx) > 0.0) { 
     }        fu=(*func)(u); 
   }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         fu=(*func)(u); 
   printf("\n#Hessian matrix#\n");        if (fu < *fc) { 
   for (i=1;i<=npar;i++) {          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     for (j=1;j<=npar;j++) {            SHFT(*fb,*fc,fu,(*func)(u)) 
       printf("%.3e ",hess[i][j]);            } 
     }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     printf("\n");        u=ulim; 
   }        fu=(*func)(u); 
       } else { 
   /* Recompute Inverse */        u=(*cx)+GOLD*(*cx-*bx); 
   for (i=1;i<=npar;i++)        fu=(*func)(u); 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      } 
   ludcmp(a,npar,indx,&pd);      SHFT(*ax,*bx,*cx,u) 
         SHFT(*fa,*fb,*fc,fu) 
   /*  printf("\n#Hessian matrix recomputed#\n");        } 
   } 
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  /*************** linmin ************************/
     x[j]=1;  
     lubksb(a,npar,indx,x);  int ncom; 
     for (i=1;i<=npar;i++){  double *pcom,*xicom;
       y[i][j]=x[i];  double (*nrfunc)(double []); 
       printf("%.3e ",y[i][j]);   
     }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     printf("\n");  { 
   }    double brent(double ax, double bx, double cx, 
   */                 double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
   free_matrix(a,1,npar,1,npar);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   free_matrix(y,1,npar,1,npar);                double *fc, double (*func)(double)); 
   free_vector(x,1,npar);    int j; 
   free_ivector(indx,1,npar);    double xx,xmin,bx,ax; 
   free_matrix(hess,1,npar,1,npar);    double fx,fb,fa;
    
     ncom=n; 
 }    pcom=vector(1,n); 
     xicom=vector(1,n); 
 /*************** hessian matrix ****************/    nrfunc=func; 
 double hessii( double x[], double delta, int theta, double delti[])    for (j=1;j<=n;j++) { 
 {      pcom[j]=p[j]; 
   int i;      xicom[j]=xi[j]; 
   int l=1, lmax=20;    } 
   double k1,k2;    ax=0.0; 
   double p2[NPARMAX+1];    xx=1.0; 
   double res;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   double fx;  #ifdef DEBUG
   int k=0,kmax=10;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   double l1;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   #endif
   fx=func(x);    for (j=1;j<=n;j++) { 
   for (i=1;i<=npar;i++) p2[i]=x[i];      xi[j] *= xmin; 
   for(l=0 ; l <=lmax; l++){      p[j] += xi[j]; 
     l1=pow(10,l);    } 
     delts=delt;    free_vector(xicom,1,n); 
     for(k=1 ; k <kmax; k=k+1){    free_vector(pcom,1,n); 
       delt = delta*(l1*k);  } 
       p2[theta]=x[theta] +delt;  
       k1=func(p2)-fx;  char *asc_diff_time(long time_sec, char ascdiff[])
       p2[theta]=x[theta]-delt;  {
       k2=func(p2)-fx;    long sec_left, days, hours, minutes;
       /*res= (k1-2.0*fx+k2)/delt/delt; */    days = (time_sec) / (60*60*24);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    sec_left = (time_sec) % (60*60*24);
          hours = (sec_left) / (60*60) ;
 #ifdef DEBUG    sec_left = (sec_left) %(60*60);
       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);    minutes = (sec_left) /60;
 #endif    sec_left = (sec_left) % (60);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    return ascdiff;
         k=kmax;  }
       }  
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  /*************** powell ************************/
         k=kmax; l=lmax*10.;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       }              double (*func)(double [])) 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  { 
         delts=delt;    void linmin(double p[], double xi[], int n, double *fret, 
       }                double (*func)(double [])); 
     }    int i,ibig,j; 
   }    double del,t,*pt,*ptt,*xit;
   delti[theta]=delts;    double fp,fptt;
   return res;    double *xits;
      int niterf, itmp;
 }  
     pt=vector(1,n); 
 double hessij( double x[], double delti[], int thetai,int thetaj)    ptt=vector(1,n); 
 {    xit=vector(1,n); 
   int i;    xits=vector(1,n); 
   int l=1, l1, lmax=20;    *fret=(*func)(p); 
   double k1,k2,k3,k4,res,fx;    for (j=1;j<=n;j++) pt[j]=p[j]; 
   double p2[NPARMAX+1];    for (*iter=1;;++(*iter)) { 
   int k;      fp=(*fret); 
       ibig=0; 
   fx=func(x);      del=0.0; 
   for (k=1; k<=2; k++) {      last_time=curr_time;
     for (i=1;i<=npar;i++) p2[i]=x[i];      (void) gettimeofday(&curr_time,&tzp);
     p2[thetai]=x[thetai]+delti[thetai]/k;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      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);
     k1=func(p2)-fx;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
       for (i=1;i<=n;i++) {
     p2[thetai]=x[thetai]+delti[thetai]/k;        printf(" %d %.12f",i, p[i]);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        fprintf(ficlog," %d %.12lf",i, p[i]);
     k2=func(p2)-fx;        fprintf(ficrespow," %.12lf", p[i]);
        }
     p2[thetai]=x[thetai]-delti[thetai]/k;      printf("\n");
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      fprintf(ficlog,"\n");
     k3=func(p2)-fx;      fprintf(ficrespow,"\n");fflush(ficrespow);
        if(*iter <=3){
     p2[thetai]=x[thetai]-delti[thetai]/k;        tm = *localtime(&curr_time.tv_sec);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        strcpy(strcurr,asctime(&tm));
     k4=func(p2)-fx;  /*       asctime_r(&tm,strcurr); */
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        forecast_time=curr_time; 
 #ifdef DEBUG        itmp = strlen(strcurr);
     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);        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
 #endif          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);
   return res;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
 }        for(niterf=10;niterf<=30;niterf+=10){
           forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
 /************** Inverse of matrix **************/          tmf = *localtime(&forecast_time.tv_sec);
 void ludcmp(double **a, int n, int *indx, double *d)  /*      asctime_r(&tmf,strfor); */
 {          strcpy(strfor,asctime(&tmf));
   int i,imax,j,k;          itmp = strlen(strfor);
   double big,dum,sum,temp;          if(strfor[itmp-1]=='\n')
   double *vv;          strfor[itmp-1]='\0';
            printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
   vv=vector(1,n);          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);
   *d=1.0;        }
   for (i=1;i<=n;i++) {      }
     big=0.0;      for (i=1;i<=n;i++) { 
     for (j=1;j<=n;j++)        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       if ((temp=fabs(a[i][j])) > big) big=temp;        fptt=(*fret); 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  #ifdef DEBUG
     vv[i]=1.0/big;        printf("fret=%lf \n",*fret);
   }        fprintf(ficlog,"fret=%lf \n",*fret);
   for (j=1;j<=n;j++) {  #endif
     for (i=1;i<j;i++) {        printf("%d",i);fflush(stdout);
       sum=a[i][j];        fprintf(ficlog,"%d",i);fflush(ficlog);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        linmin(p,xit,n,fret,func); 
       a[i][j]=sum;        if (fabs(fptt-(*fret)) > del) { 
     }          del=fabs(fptt-(*fret)); 
     big=0.0;          ibig=i; 
     for (i=j;i<=n;i++) {        } 
       sum=a[i][j];  #ifdef DEBUG
       for (k=1;k<j;k++)        printf("%d %.12e",i,(*fret));
         sum -= a[i][k]*a[k][j];        fprintf(ficlog,"%d %.12e",i,(*fret));
       a[i][j]=sum;        for (j=1;j<=n;j++) {
       if ( (dum=vv[i]*fabs(sum)) >= big) {          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         big=dum;          printf(" x(%d)=%.12e",j,xit[j]);
         imax=i;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       }        }
     }        for(j=1;j<=n;j++) {
     if (j != imax) {          printf(" p=%.12e",p[j]);
       for (k=1;k<=n;k++) {          fprintf(ficlog," p=%.12e",p[j]);
         dum=a[imax][k];        }
         a[imax][k]=a[j][k];        printf("\n");
         a[j][k]=dum;        fprintf(ficlog,"\n");
       }  #endif
       *d = -(*d);      } 
       vv[imax]=vv[j];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     }  #ifdef DEBUG
     indx[j]=imax;        int k[2],l;
     if (a[j][j] == 0.0) a[j][j]=TINY;        k[0]=1;
     if (j != n) {        k[1]=-1;
       dum=1.0/(a[j][j]);        printf("Max: %.12e",(*func)(p));
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        fprintf(ficlog,"Max: %.12e",(*func)(p));
     }        for (j=1;j<=n;j++) {
   }          printf(" %.12e",p[j]);
   free_vector(vv,1,n);  /* Doesn't work */          fprintf(ficlog," %.12e",p[j]);
 ;        }
 }        printf("\n");
         fprintf(ficlog,"\n");
 void lubksb(double **a, int n, int *indx, double b[])        for(l=0;l<=1;l++) {
 {          for (j=1;j<=n;j++) {
   int i,ii=0,ip,j;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   double sum;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[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]);
   for (i=1;i<=n;i++) {          }
     ip=indx[i];          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     sum=b[ip];          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     b[ip]=b[i];        }
     if (ii)  #endif
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  
     else if (sum) ii=i;  
     b[i]=sum;        free_vector(xit,1,n); 
   }        free_vector(xits,1,n); 
   for (i=n;i>=1;i--) {        free_vector(ptt,1,n); 
     sum=b[i];        free_vector(pt,1,n); 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        return; 
     b[i]=sum/a[i][i];      } 
   }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 }      for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
 /************ Frequencies ********************/        xit[j]=p[j]-pt[j]; 
 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)        pt[j]=p[j]; 
 {  /* Some frequencies */      } 
        fptt=(*func)(ptt); 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;      if (fptt < fp) { 
   double ***freq; /* Frequencies */        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   double *pp;        if (t < 0.0) { 
   double pos, k2, dateintsum=0,k2cpt=0;          linmin(p,xit,n,fret,func); 
   FILE *ficresp;          for (j=1;j<=n;j++) { 
   char fileresp[FILENAMELENGTH];            xi[j][ibig]=xi[j][n]; 
              xi[j][n]=xit[j]; 
   pp=vector(1,nlstate);          }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  #ifdef DEBUG
   strcpy(fileresp,"p");          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   strcat(fileresp,fileres);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   if((ficresp=fopen(fileresp,"w"))==NULL) {          for(j=1;j<=n;j++){
     printf("Problem with prevalence resultfile: %s\n", fileresp);            printf(" %.12e",xit[j]);
     exit(0);            fprintf(ficlog," %.12e",xit[j]);
   }          }
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          printf("\n");
   j1=0;          fprintf(ficlog,"\n");
   #endif
   j=cptcoveff;        }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      } 
     } 
   for(k1=1; k1<=j;k1++){  } 
    for(i1=1; i1<=ncodemax[k1];i1++){  
        j1++;  /**** Prevalence limit (stable or period prevalence)  ****************/
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  
          scanf("%d", i);*/  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         for (i=-1; i<=nlstate+ndeath; i++)    {
          for (jk=-1; jk<=nlstate+ndeath; jk++)      /* Computes the prevalence limit in each live state at age x by left multiplying the unit
            for(m=agemin; m <= agemax+3; m++)       matrix by transitions matrix until convergence is reached */
              freq[i][jk][m]=0;  
     int i, ii,j,k;
         dateintsum=0;    double min, max, maxmin, maxmax,sumnew=0.;
         k2cpt=0;    double **matprod2();
        for (i=1; i<=imx; i++) {    double **out, cov[NCOVMAX+1], **pmij();
          bool=1;    double **newm;
          if  (cptcovn>0) {    double agefin, delaymax=50 ; /* Max number of years to converge */
            for (z1=1; z1<=cptcoveff; z1++)  
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    for (ii=1;ii<=nlstate+ndeath;ii++)
                bool=0;      for (j=1;j<=nlstate+ndeath;j++){
          }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
          if (bool==1) {      }
            for(m=firstpass; m<=lastpass; m++){  
              k2=anint[m][i]+(mint[m][i]/12.);     cov[1]=1.;
              if ((k2>=dateprev1) && (k2<=dateprev2)) {   
                if(agev[m][i]==0) agev[m][i]=agemax+1;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
                if(agev[m][i]==1) agev[m][i]=agemax+2;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      newm=savm;
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      /* Covariates have to be included here again */
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {       cov[2]=agefin;
                  dateintsum=dateintsum+k2;    
                  k2cpt++;        for (k=1; k<=cptcovn;k++) {
                }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
              }        }
            }        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
          }        for (k=1; k<=cptcovprod;k++)
        }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
          
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         if  (cptcovn>0) {        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
          fprintf(ficresp, "\n#********** Variable ");      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
        fprintf(ficresp, "**********\n#");      savm=oldm;
         }      oldm=newm;
        for(i=1; i<=nlstate;i++)      maxmax=0.;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      for(j=1;j<=nlstate;j++){
        fprintf(ficresp, "\n");        min=1.;
                max=0.;
   for(i=(int)agemin; i <= (int)agemax+3; i++){        for(i=1; i<=nlstate; i++) {
     if(i==(int)agemax+3)          sumnew=0;
       printf("Total");          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     else          prlim[i][j]= newm[i][j]/(1-sumnew);
       printf("Age %d", i);          max=FMAX(max,prlim[i][j]);
     for(jk=1; jk <=nlstate ; jk++){          min=FMIN(min,prlim[i][j]);
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        }
         pp[jk] += freq[jk][m][i];        maxmin=max-min;
     }        maxmax=FMAX(maxmax,maxmin);
     for(jk=1; jk <=nlstate ; jk++){      }
       for(m=-1, pos=0; m <=0 ; m++)      if(maxmax < ftolpl){
         pos += freq[jk][m][i];        return prlim;
       if(pp[jk]>=1.e-10)      }
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    }
       else  }
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  
     }  /*************** transition probabilities ***************/ 
   
      for(jk=1; jk <=nlstate ; jk++){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  {
         pp[jk] += freq[jk][m][i];    double s1, s2;
      }    /*double t34;*/
     int i,j,j1, nc, ii, jj;
     for(jk=1,pos=0; jk <=nlstate ; jk++)  
       pos += pp[jk];      for(i=1; i<= nlstate; i++){
     for(jk=1; jk <=nlstate ; jk++){        for(j=1; j<i;j++){
       if(pos>=1.e-5)          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            /*s2 += param[i][j][nc]*cov[nc];*/
       else            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
       if( i <= (int) agemax){          }
         if(pos>=1.e-5){          ps[i][j]=s2;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
           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]);*/        for(j=i+1; j<=nlstate+ndeath;j++){
         }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       else            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
       }          }
     }          ps[i][j]=s2;
     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]);      /*ps[3][2]=1;*/
     if(i <= (int) agemax)      
       fprintf(ficresp,"\n");      for(i=1; i<= nlstate; i++){
     printf("\n");        s1=0;
     }        for(j=1; j<i; j++){
     }          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); */
   dateintmean=dateintsum/k2cpt;        }
          for(j=i+1; j<=nlstate+ndeath; j++){
   fclose(ficresp);          s1+=exp(ps[i][j]);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   free_vector(pp,1,nlstate);        }
         ps[i][i]=1./(s1+1.);
   /* End of Freq */        for(j=1; j<i; j++)
 }          ps[i][j]= exp(ps[i][j])*ps[i][i];
         for(j=i+1; j<=nlstate+ndeath; j++)
 /************ Prevalence ********************/          ps[i][j]= exp(ps[i][j])*ps[i][i];
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
 {  /* Some frequencies */      } /* end i */
        
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   double ***freq; /* Frequencies */        for(jj=1; jj<= nlstate+ndeath; jj++){
   double *pp;          ps[ii][jj]=0;
   double pos, k2;          ps[ii][ii]=1;
         }
   pp=vector(1,nlstate);      }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      
    
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
   j1=0;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
    /*         printf("ddd %lf ",ps[ii][jj]); */
   j=cptcoveff;  /*       } */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  /*       printf("\n "); */
    /*        } */
  for(k1=1; k1<=j;k1++){  /*        printf("\n ");printf("%lf ",cov[2]); */
     for(i1=1; i1<=ncodemax[k1];i1++){         /*
       j1++;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
          goto end;*/
       for (i=-1; i<=nlstate+ndeath; i++)        return ps;
         for (jk=-1; jk<=nlstate+ndeath; jk++)    }
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;  /**************** Product of 2 matrices ******************/
        
       for (i=1; i<=imx; i++) {  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
         bool=1;  {
         if  (cptcovn>0) {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
           for (z1=1; z1<=cptcoveff; z1++)       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    /* in, b, out are matrice of pointers which should have been initialized 
               bool=0;       before: only the contents of out is modified. The function returns
         }       a pointer to pointers identical to out */
         if (bool==1) {    long i, j, k;
           for(m=firstpass; m<=lastpass; m++){    for(i=nrl; i<= nrh; i++)
             k2=anint[m][i]+(mint[m][i]/12.);      for(k=ncolol; k<=ncoloh; k++)
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        for(j=ncl,out[i][k]=0.; j<=nch; j++)
               if(agev[m][i]==0) agev[m][i]=agemax+1;          out[i][k] +=in[i][j]*b[j][k];
               if(agev[m][i]==1) agev[m][i]=agemax+2;  
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    return out;
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */  }
             }  
           }  
         }  /************* Higher Matrix Product ***************/
       }  
         for(i=(int)agemin; i <= (int)agemax+3; i++){  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
           for(jk=1; jk <=nlstate ; jk++){  {
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    /* Computes the transition matrix starting at age 'age' over 
               pp[jk] += freq[jk][m][i];       'nhstepm*hstepm*stepm' months (i.e. until
           }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
           for(jk=1; jk <=nlstate ; jk++){       nhstepm*hstepm matrices. 
             for(m=-1, pos=0; m <=0 ; m++)       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
             pos += freq[jk][m][i];       (typically every 2 years instead of every month which is too big 
         }       for the memory).
               Model is determined by parameters x and covariates have to be 
          for(jk=1; jk <=nlstate ; jk++){       included manually here. 
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
              pp[jk] += freq[jk][m][i];       */
          }  
              int i, j, d, h, k;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    double **out, cov[NCOVMAX+1];
     double **newm;
          for(jk=1; jk <=nlstate ; jk++){            
            if( i <= (int) agemax){    /* Hstepm could be zero and should return the unit matrix */
              if(pos>=1.e-5){    for (i=1;i<=nlstate+ndeath;i++)
                probs[i][jk][j1]= pp[jk]/pos;      for (j=1;j<=nlstate+ndeath;j++){
              }        oldm[i][j]=(i==j ? 1.0 : 0.0);
            }        po[i][j][0]=(i==j ? 1.0 : 0.0);
          }      }
              /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         }    for(h=1; h <=nhstepm; h++){
     }      for(d=1; d <=hstepm; d++){
   }        newm=savm;
          /* Covariates have to be included here again */
          cov[1]=1.;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   free_vector(pp,1,nlstate);        for (k=1; k<=cptcovn;k++) 
            cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 }  /* End of Freq */        for (k=1; k<=cptcovage;k++)
           cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 /************* Waves Concatenation ***************/        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]]];
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  
 {  
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
      Death is a valid wave (if date is known).        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]                     pmij(pmmij,cov,ncovmodel,x,nlstate));
      and mw[mi+1][i]. dh depends on stepm.        savm=oldm;
      */        oldm=newm;
       }
   int i, mi, m;      for(i=1; i<=nlstate+ndeath; i++)
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        for(j=1;j<=nlstate+ndeath;j++) {
      double sum=0., jmean=0.;*/          po[i][j][h]=newm[i][j];
           /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   int j, k=0,jk, ju, jl;        }
   double sum=0.;      /*printf("h=%d ",h);*/
   jmin=1e+5;    } /* end h */
   jmax=-1;  /*     printf("\n H=%d \n",h); */
   jmean=0.;    return po;
   for(i=1; i<=imx; i++){  }
     mi=0;  
     m=firstpass;  
     while(s[m][i] <= nlstate){  /*************** log-likelihood *************/
       if(s[m][i]>=1)  double func( double *x)
         mw[++mi][i]=m;  {
       if(m >=lastpass)    int i, ii, j, k, mi, d, kk;
         break;    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
       else    double **out;
         m++;    double sw; /* Sum of weights */
     }/* end while */    double lli; /* Individual log likelihood */
     if (s[m][i] > nlstate){    int s1, s2;
       mi++;     /* Death is another wave */    double bbh, survp;
       /* if(mi==0)  never been interviewed correctly before death */    long ipmx;
          /* Only death is a correct wave */    /*extern weight */
       mw[mi][i]=m;    /* We are differentiating ll according to initial status */
     }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
     wav[i]=mi;      printf(" %d\n",s[4][i]);
     if(mi==0)    */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    cov[1]=1.;
   }  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
   for(i=1; i<=imx; i++){  
     for(mi=1; mi<wav[i];mi++){    if(mle==1){
       if (stepm <=0)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         dh[mi][i]=1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       else{        for(mi=1; mi<= wav[i]-1; mi++){
         if (s[mw[mi+1][i]][i] > nlstate) {          for (ii=1;ii<=nlstate+ndeath;ii++)
           if (agedc[i] < 2*AGESUP) {            for (j=1;j<=nlstate+ndeath;j++){
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           if(j==0) j=1;  /* Survives at least one month after exam */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           k=k+1;            }
           if (j >= jmax) jmax=j;          for(d=0; d<dh[mi][i]; d++){
           if (j <= jmin) jmin=j;            newm=savm;
           sum=sum+j;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           /*if (j<0) printf("j=%d num=%d \n",j,i); */            for (kk=1; kk<=cptcovage;kk++) {
           }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }            }
         else{            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           k=k+1;            savm=oldm;
           if (j >= jmax) jmax=j;            oldm=newm;
           else if (j <= jmin)jmin=j;          } /* end mult */
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        
           sum=sum+j;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         }          /* But now since version 0.9 we anticipate for bias at large stepm.
         jk= j/stepm;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         jl= j -jk*stepm;           * (in months) between two waves is not a multiple of stepm, we rounded to 
         ju= j -(jk+1)*stepm;           * the nearest (and in case of equal distance, to the lowest) interval but now
         if(jl <= -ju)           * we keep into memory the bias bh[mi][i] and also the previous matrix product
           dh[mi][i]=jk;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         else           * probability in order to take into account the bias as a fraction of the way
           dh[mi][i]=jk+1;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
         if(dh[mi][i]==0)           * -stepm/2 to stepm/2 .
           dh[mi][i]=1; /* At least one step */           * For stepm=1 the results are the same as for previous versions of Imach.
       }           * For stepm > 1 the results are less biased than in previous versions. 
     }           */
   }          s1=s[mw[mi][i]][i];
   jmean=sum/k;          s2=s[mw[mi+1][i]][i];
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          bbh=(double)bh[mi][i]/(double)stepm; 
  }          /* bias bh is positive if real duration
 /*********** Tricode ****************************/           * is higher than the multiple of stepm and negative otherwise.
 void tricode(int *Tvar, int **nbcode, int imx)           */
 {          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   int Ndum[20],ij=1, k, j, i;          if( s2 > nlstate){ 
   int cptcode=0;            /* i.e. if s2 is a death state and if the date of death is known 
   cptcoveff=0;               then the contribution to the likelihood is the probability to 
                 die between last step unit time and current  step unit time, 
   for (k=0; k<19; k++) Ndum[k]=0;               which is also equal to probability to die before dh 
   for (k=1; k<=7; k++) ncodemax[k]=0;               minus probability to die before dh-stepm . 
                In version up to 0.92 likelihood was computed
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          as if date of death was unknown. Death was treated as any other
     for (i=1; i<=imx; i++) {          health state: the date of the interview describes the actual state
       ij=(int)(covar[Tvar[j]][i]);          and not the date of a change in health state. The former idea was
       Ndum[ij]++;          to consider that at each interview the state was recorded
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          (healthy, disable or death) and IMaCh was corrected; but when we
       if (ij > cptcode) cptcode=ij;          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
     for (i=0; i<=cptcode; i++) {          stepm. It is no more the probability to die between last interview
       if(Ndum[i]!=0) ncodemax[j]++;          and month of death but the probability to survive from last
     }          interview up to one month before death multiplied by the
     ij=1;          probability to die within a month. Thanks to Chris
           Jackson for correcting this bug.  Former versions increased
           mortality artificially. The bad side is that we add another loop
     for (i=1; i<=ncodemax[j]; i++) {          which slows down the processing. The difference can be up to 10%
       for (k=0; k<=19; k++) {          lower mortality.
         if (Ndum[k] != 0) {            */
           nbcode[Tvar[j]][ij]=k;            lli=log(out[s1][s2] - savm[s1][s2]);
           ij++;  
         }  
         if (ij > ncodemax[j]) break;          } else if  (s2==-2) {
       }              for (j=1,survp=0. ; j<=nlstate; j++) 
     }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   }              /*survp += out[s1][j]; */
             lli= log(survp);
  for (k=0; k<19; k++) Ndum[k]=0;          }
           
  for (i=1; i<=ncovmodel-2; i++) {          else if  (s2==-4) { 
       ij=Tvar[i];            for (j=3,survp=0. ; j<=nlstate; j++)  
       Ndum[ij]++;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     }            lli= log(survp); 
           } 
  ij=1;  
  for (i=1; i<=10; i++) {          else if  (s2==-5) { 
    if((Ndum[i]!=0) && (i<=ncov)){            for (j=1,survp=0. ; j<=2; j++)  
      Tvaraff[ij]=i;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
      ij++;            lli= log(survp); 
    }          } 
  }          
            else{
     cptcoveff=ij-1;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
           } 
 /*********** Health Expectancies ****************/          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
 {          ipmx +=1;
   /* Health expectancies */          sw += weight[i];
   int i, j, nhstepm, hstepm, h;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double age, agelim,hf;        } /* end of wave */
   double ***p3mat;      } /* end of individual */
      }  else if(mle==2){
   fprintf(ficreseij,"# Health expectancies\n");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   fprintf(ficreseij,"# Age");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for(i=1; i<=nlstate;i++)        for(mi=1; mi<= wav[i]-1; mi++){
     for(j=1; j<=nlstate;j++)          for (ii=1;ii<=nlstate+ndeath;ii++)
       fprintf(ficreseij," %1d-%1d",i,j);            for (j=1;j<=nlstate+ndeath;j++){
   fprintf(ficreseij,"\n");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   hstepm=1*YEARM; /*  Every j years of age (in month) */            }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
   agelim=AGESUP;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            for (kk=1; kk<=cptcovage;kk++) {
     /* nhstepm age range expressed in number of stepm */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);            }
     /* Typically if 20 years = 20*12/6=40 stepm */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     /*if (stepm >= YEARM) hstepm=1;*/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 hstepm=1;            savm=oldm;
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */            oldm=newm;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          } /* end mult */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          s1=s[mw[mi][i]][i];
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            s2=s[mw[mi+1][i]][i];
 hf=stepm/YEARM;          bbh=(double)bh[mi][i]/(double)stepm; 
 /*printf("stepm=%d nhstepm=%d hstepm=%d age=%lf ",stepm, nhstepm, hstepm, age);*/          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<=nlstate;i++)          ipmx +=1;
       for(j=1; j<=nlstate;j++)          sw += weight[i];
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           eij[i][j][(int)age] +=hf*(p3mat[i][j][h]+p3mat[i][j][h+1])/2.0;        } /* end of wave */
         }      } /* end of individual */
        }  else if(mle==3){  /* exponential inter-extrapolation */
     /* hf=1;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
        if (stepm >= YEARM) hf=stepm/YEARM;*/        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 hf=stepm/YEARM;        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
     fprintf(ficreseij,"%3.0f",age );            for (j=1;j<=nlstate+ndeath;j++){
     for(i=1; i<=nlstate;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<=nlstate;j++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);            }
       }          for(d=0; d<dh[mi][i]; d++){
     fprintf(ficreseij,"\n");            newm=savm;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            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];
             }
 /************ Variance ******************/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 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)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 {            savm=oldm;
   /* Variance of health expectancies */            oldm=newm;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          } /* end mult */
   double **newm;        
   double **dnewm,**doldm;          s1=s[mw[mi][i]][i];
   int i, j, nhstepm, hstepm, h;          s2=s[mw[mi+1][i]][i];
   int k, cptcode;          bbh=(double)bh[mi][i]/(double)stepm; 
   double *xp;          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 */
   double **gp, **gm;          ipmx +=1;
   double ***gradg, ***trgradg;          sw += weight[i];
   double ***p3mat;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double age,agelim;        } /* end of wave */
   int theta;      } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
    fprintf(ficresvij,"# Covariances of life expectancies\n");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   fprintf(ficresvij,"# Age");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for(i=1; i<=nlstate;i++)        for(mi=1; mi<= wav[i]-1; mi++){
     for(j=1; j<=nlstate;j++)          for (ii=1;ii<=nlstate+ndeath;ii++)
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            for (j=1;j<=nlstate+ndeath;j++){
   fprintf(ficresvij,"\n");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   xp=vector(1,npar);            }
   dnewm=matrix(1,nlstate,1,npar);          for(d=0; d<dh[mi][i]; d++){
   doldm=matrix(1,nlstate,1,nlstate);            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   hstepm=1*YEARM; /* Every year of age */            for (kk=1; kk<=cptcovage;kk++) {
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   agelim = AGESUP;            }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     if (stepm >= YEARM) hstepm=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            savm=oldm;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            oldm=newm;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          } /* end mult */
     gp=matrix(0,nhstepm,1,nlstate);        
     gm=matrix(0,nhstepm,1,nlstate);          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
     for(theta=1; theta <=npar; theta++){          if( s2 > nlstate){ 
       for(i=1; i<=npar; i++){ /* Computes gradient */            lli=log(out[s1][s2] - savm[s1][s2]);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          }else{
       }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          ipmx +=1;
           sw += weight[i];
       if (popbased==1) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for(i=1; i<=nlstate;i++)  /*      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]); */
           prlim[i][i]=probs[(int)age][i][ij];        } /* end of wave */
       }      } /* end of individual */
      }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for(j=1; j<= nlstate; j++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for(h=0; h<=nhstepm; h++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        for(mi=1; mi<= wav[i]-1; mi++){
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          for (ii=1;ii<=nlstate+ndeath;ii++)
         }            for (j=1;j<=nlstate+ndeath;j++){
       }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                  savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1; i<=npar; i++) /* Computes gradient */            }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          for(d=0; d<dh[mi][i]; d++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              newm=savm;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
       if (popbased==1) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for(i=1; i<=nlstate;i++)            }
           prlim[i][i]=probs[(int)age][i][ij];          
       }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(j=1; j<= nlstate; j++){            savm=oldm;
         for(h=0; h<=nhstepm; h++){            oldm=newm;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          } /* end mult */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        
         }          s1=s[mw[mi][i]][i];
       }          s2=s[mw[mi+1][i]][i];
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       for(j=1; j<= nlstate; j++)          ipmx +=1;
         for(h=0; h<=nhstepm; h++){          sw += weight[i];
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          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 theta */        } /* end of wave */
       } /* end of individual */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     for(h=0; h<=nhstepm; h++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       for(j=1; j<=nlstate;j++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         for(theta=1; theta <=npar; theta++)    return -l;
           trgradg[h][j][theta]=gradg[h][theta][j];  }
   
     for(i=1;i<=nlstate;i++)  /*************** log-likelihood *************/
       for(j=1;j<=nlstate;j++)  double funcone( double *x)
         vareij[i][j][(int)age] =0.;  {
     for(h=0;h<=nhstepm;h++){    /* Same as likeli but slower because of a lot of printf and if */
       for(k=0;k<=nhstepm;k++){    int i, ii, j, k, mi, d, kk;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    double **out;
         for(i=1;i<=nlstate;i++)    double lli; /* Individual log likelihood */
           for(j=1;j<=nlstate;j++)    double llt;
             vareij[i][j][(int)age] += doldm[i][j];    int s1, s2;
       }    double bbh, survp;
     }    /*extern weight */
     h=1;    /* We are differentiating ll according to initial status */
     if (stepm >= YEARM) h=stepm/YEARM;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     fprintf(ficresvij,"%.0f ",age );    /*for(i=1;i<imx;i++) 
     for(i=1; i<=nlstate;i++)      printf(" %d\n",s[4][i]);
       for(j=1; j<=nlstate;j++){    */
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    cov[1]=1.;
       }  
     fprintf(ficresvij,"\n");    for(k=1; k<=nlstate; k++) ll[k]=0.;
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      for(mi=1; mi<= wav[i]-1; mi++){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (ii=1;ii<=nlstate+ndeath;ii++)
   } /* End age */          for (j=1;j<=nlstate+ndeath;j++){
              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(xp,1,npar);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_matrix(doldm,1,nlstate,1,npar);          }
   free_matrix(dnewm,1,nlstate,1,nlstate);        for(d=0; d<dh[mi][i]; d++){
           newm=savm;
 }          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
 /************ Variance of prevlim ******************/            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 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)          }
 {          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* Variance of prevalence limit */                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          savm=oldm;
   double **newm;          oldm=newm;
   double **dnewm,**doldm;        } /* end mult */
   int i, j, nhstepm, hstepm;        
   int k, cptcode;        s1=s[mw[mi][i]][i];
   double *xp;        s2=s[mw[mi+1][i]][i];
   double *gp, *gm;        bbh=(double)bh[mi][i]/(double)stepm; 
   double **gradg, **trgradg;        /* bias is positive if real duration
   double age,agelim;         * is higher than the multiple of stepm and negative otherwise.
   int theta;         */
            if( s2 > nlstate && (mle <5) ){  /* Jackson */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          lli=log(out[s1][s2] - savm[s1][s2]);
   fprintf(ficresvpl,"# Age");        } else if  (s2==-2) {
   for(i=1; i<=nlstate;i++)          for (j=1,survp=0. ; j<=nlstate; j++) 
       fprintf(ficresvpl," %1d-%1d",i,i);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   fprintf(ficresvpl,"\n");          lli= log(survp);
         }else if (mle==1){
   xp=vector(1,npar);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   dnewm=matrix(1,nlstate,1,npar);        } else if(mle==2){
   doldm=matrix(1,nlstate,1,nlstate);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
          } else if(mle==3){  /* exponential inter-extrapolation */
   hstepm=1*YEARM; /* Every year of age */          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 */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   agelim = AGESUP;          lli=log(out[s1][s2]); /* Original formula */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        } else{  /* mle=0 back to 1 */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     if (stepm >= YEARM) hstepm=1;          /*lli=log(out[s1][s2]); */ /* Original formula */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        } /* End of if */
     gradg=matrix(1,npar,1,nlstate);        ipmx +=1;
     gp=vector(1,nlstate);        sw += weight[i];
     gm=vector(1,nlstate);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     for(theta=1; theta <=npar; theta++){        if(globpr){
       for(i=1; i<=npar; i++){ /* Computes gradient */          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
         xp[i] = x[i] + (i==theta ?delti[theta]:0);   %11.6f %11.6f %11.6f ", \
       }                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
       for(i=1;i<=nlstate;i++)          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
         gp[i] = prlim[i][i];            llt +=ll[k]*gipmx/gsw;
                fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
       for(i=1; i<=npar; i++) /* Computes gradient */          }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          fprintf(ficresilk," %10.6f\n", -llt);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        }
       for(i=1;i<=nlstate;i++)      } /* end of wave */
         gm[i] = prlim[i][i];    } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       for(i=1;i<=nlstate;i++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     } /* End theta */    if(globpr==0){ /* First time we count the contributions and weights */
       gipmx=ipmx;
     trgradg =matrix(1,nlstate,1,npar);      gsw=sw;
     }
     for(j=1; j<=nlstate;j++)    return -l;
       for(theta=1; theta <=npar; theta++)  }
         trgradg[j][theta]=gradg[theta][j];  
   
     for(i=1;i<=nlstate;i++)  /*************** function likelione ***********/
       varpl[i][(int)age] =0.;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  {
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    /* This routine should help understanding what is done with 
     for(i=1;i<=nlstate;i++)       the selection of individuals/waves and
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */       to check the exact contribution to the likelihood.
        Plotting could be done.
     fprintf(ficresvpl,"%.0f ",age );     */
     for(i=1; i<=nlstate;i++)    int k;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  
     fprintf(ficresvpl,"\n");    if(*globpri !=0){ /* Just counts and sums, no printings */
     free_vector(gp,1,nlstate);      strcpy(fileresilk,"ilk"); 
     free_vector(gm,1,nlstate);      strcat(fileresilk,fileres);
     free_matrix(gradg,1,npar,1,nlstate);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     free_matrix(trgradg,1,nlstate,1,npar);        printf("Problem with resultfile: %s\n", fileresilk);
   } /* End age */        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
   free_vector(xp,1,npar);      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");
   free_matrix(doldm,1,nlstate,1,npar);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   free_matrix(dnewm,1,nlstate,1,nlstate);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(k=1; k<=nlstate; k++) 
 }        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
 /************ Variance of one-step probabilities  ******************/    }
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)  
 {    *fretone=(*funcone)(p);
   int i, j;    if(*globpri !=0){
   int k=0, cptcode;      fclose(ficresilk);
   double **dnewm,**doldm;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   double *xp;      fflush(fichtm); 
   double *gp, *gm;    } 
   double **gradg, **trgradg;    return;
   double age,agelim, cov[NCOVMAX];  }
   int theta;  
   char fileresprob[FILENAMELENGTH];  
   /*********** Maximum Likelihood Estimation ***************/
   strcpy(fileresprob,"prob");  
   strcat(fileresprob,fileres);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  {
     printf("Problem with resultfile: %s\n", fileresprob);    int i,j, iter;
   }    double **xi;
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    double fret;
      double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
   xp=vector(1,npar);    xi=matrix(1,npar,1,npar);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    for (i=1;i<=npar;i++)
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      for (j=1;j<=npar;j++)
          xi[i][j]=(i==j ? 1.0 : 0.0);
   cov[1]=1;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   for (age=bage; age<=fage; age ++){    strcpy(filerespow,"pow"); 
     cov[2]=age;    strcat(filerespow,fileres);
     gradg=matrix(1,npar,1,9);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     trgradg=matrix(1,9,1,npar);      printf("Problem with resultfile: %s\n", filerespow);
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    }
        fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for(theta=1; theta <=npar; theta++){    for (i=1;i<=nlstate;i++)
       for(i=1; i<=npar; i++)      for(j=1;j<=nlstate+ndeath;j++)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
          fprintf(ficrespow,"\n");
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  
        powell(p,xi,npar,ftol,&iter,&fret,func);
       k=0;  
       for(i=1; i<= (nlstate+ndeath); i++){    free_matrix(xi,1,npar,1,npar);
         for(j=1; j<=(nlstate+ndeath);j++){    fclose(ficrespow);
            k=k+1;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
           gp[k]=pmmij[i][j];    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         }    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       }  
   }
       for(i=1; i<=npar; i++)  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  /**** Computes Hessian and covariance matrix ***/
      void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   {
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    double  **a,**y,*x,pd;
       k=0;    double **hess;
       for(i=1; i<=(nlstate+ndeath); i++){    int i, j,jk;
         for(j=1; j<=(nlstate+ndeath);j++){    int *indx;
           k=k+1;  
           gm[k]=pmmij[i][j];    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
         }    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
       }    void lubksb(double **a, int npar, int *indx, double b[]) ;
          void ludcmp(double **a, int npar, int *indx, double *d) ;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    double gompertz(double p[]);
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      hess=matrix(1,npar,1,npar);
     }  
     printf("\nCalculation of the hessian matrix. Wait...\n");
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       for(theta=1; theta <=npar; theta++)    for (i=1;i<=npar;i++){
       trgradg[j][theta]=gradg[theta][j];      printf("%d",i);fflush(stdout);
        fprintf(ficlog,"%d",i);fflush(ficlog);
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);     
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       
      pmij(pmmij,cov,ncovmodel,x,nlstate);      /*  printf(" %f ",p[i]);
           printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
      k=0;    }
      for(i=1; i<=(nlstate+ndeath); i++){    
        for(j=1; j<=(nlstate+ndeath);j++){    for (i=1;i<=npar;i++) {
          k=k+1;      for (j=1;j<=npar;j++)  {
          gm[k]=pmmij[i][j];        if (j>i) { 
         }          printf(".%d%d",i,j);fflush(stdout);
      }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
                hess[i][j]=hessij(p,delti,i,j,func,npar);
      /*printf("\n%d ",(int)age);          
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          hess[j][i]=hess[i][j];    
                  /*printf(" %lf ",hess[i][j]);*/
         }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      }
      }*/    }
     printf("\n");
   fprintf(ficresprob,"\n%d ",(int)age);    fprintf(ficlog,"\n");
   
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    
   }    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    x=vector(1,npar);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    indx=ivector(1,npar);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    for (i=1;i<=npar;i++)
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
 }    ludcmp(a,npar,indx,&pd);
  free_vector(xp,1,npar);  
 fclose(ficresprob);    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
 }      x[j]=1;
       lubksb(a,npar,indx,x);
 /******************* Printing html file ***********/      for (i=1;i<=npar;i++){ 
 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 optionfile[],char optionfilehtm[],char rfileres[] ){        matcov[i][j]=x[i];
   int jj1, k1, i1, cpt;      }
   FILE *fichtm;    }
   /*char optionfilehtm[FILENAMELENGTH];*/  
     printf("\n#Hessian matrix#\n");
   strcpy(optionfilehtm,optionfile);    fprintf(ficlog,"\n#Hessian matrix#\n");
   strcat(optionfilehtm,".htm");    for (i=1;i<=npar;i++) { 
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      for (j=1;j<=npar;j++) { 
     printf("Problem with %s \n",optionfilehtm), exit(0);        printf("%.3e ",hess[i][j]);
   }        fprintf(ficlog,"%.3e ",hess[i][j]);
       }
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71 </font> <hr size=\"2\" color=\"#EC5E5E\">      printf("\n");
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>      fprintf(ficlog,"\n");
     }
 Total number of observations=%d <br>  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>    /* Recompute Inverse */
 <hr  size=\"2\" color=\"#EC5E5E\">    for (i=1;i<=npar;i++)
 <li>Outputs files<br><br>\n      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    ludcmp(a,npar,indx,&pd);
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>  
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    /*  printf("\n#Hessian matrix recomputed#\n");
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>  
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    for (j=1;j<=npar;j++) {
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>      for (i=1;i<=npar;i++) x[i]=0;
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>      x[j]=1;
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>      lubksb(a,npar,indx,x);
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>      for (i=1;i<=npar;i++){ 
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>        y[i][j]=x[i];
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>        printf("%.3e ",y[i][j]);
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);        fprintf(ficlog,"%.3e ",y[i][j]);
        }
 fprintf(fichtm," <li>Graphs</li><p>");      printf("\n");
       fprintf(ficlog,"\n");
  m=cptcoveff;    }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    */
   
  jj1=0;    free_matrix(a,1,npar,1,npar);
  for(k1=1; k1<=m;k1++){    free_matrix(y,1,npar,1,npar);
    for(i1=1; i1<=ncodemax[k1];i1++){    free_vector(x,1,npar);
        jj1++;    free_ivector(indx,1,npar);
        if (cptcovn > 0) {    free_matrix(hess,1,npar,1,npar);
          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\">");  
        }  /*************** hessian matrix ****************/
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      {
        for(cpt=1; cpt<nlstate;cpt++){    int i;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    int l=1, lmax=20;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    double k1,k2;
        }    double p2[MAXPARM+1]; /* identical to x */
     for(cpt=1; cpt<=nlstate;cpt++) {    double res;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
 interval) in state (%d): v%s%d%d.gif <br>    double fx;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      int k=0,kmax=10;
      }    double l1;
      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>    fx=func(x);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    for (i=1;i<=npar;i++) p2[i]=x[i];
      }    for(l=0 ; l <=lmax; l++){
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      l1=pow(10,l);
 health expectancies in states (1) and (2): e%s%d.gif<br>      delts=delt;
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      for(k=1 ; k <kmax; k=k+1){
 fprintf(fichtm,"\n</body>");        delt = delta*(l1*k);
    }        p2[theta]=x[theta] +delt;
    }        k1=func(p2)-fx;
 fclose(fichtm);        p2[theta]=x[theta]-delt;
 }        k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
 /******************* Gnuplot file **************/        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){        
   #ifdef DEBUGHESS
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   strcpy(optionfilegnuplot,optionfilefiname);  #endif
   strcat(optionfilegnuplot,".plt");        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     printf("Problem with file %s",optionfilegnuplot);          k=kmax;
   }        }
         else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 #ifdef windows          k=kmax; l=lmax*10.;
     fprintf(ficgp,"cd \"%s\" \n",pathc);        }
 #endif        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
 m=pow(2,cptcoveff);          delts=delt;
          }
  /* 1eme*/      }
   for (cpt=1; cpt<= nlstate ; cpt ++) {    }
    for (k1=1; k1<= m ; k1 ++) {    delti[theta]=delts;
     return res; 
 #ifdef windows    
     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",agemin,fage,fileres,k1-1,k1-1);  }
 #endif  
 #ifdef unix  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);  {
 #endif    int i;
     int l=1, l1, lmax=20;
 for (i=1; i<= nlstate ; i ++) {    double k1,k2,k3,k4,res,fx;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double p2[MAXPARM+1];
   else fprintf(ficgp," \%%*lf (\%%*lf)");    int k;
 }  
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    fx=func(x);
     for (i=1; i<= nlstate ; i ++) {    for (k=1; k<=2; k++) {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for (i=1;i<=npar;i++) p2[i]=x[i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");      p2[thetai]=x[thetai]+delti[thetai]/k;
 }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      k1=func(p2)-fx;
      for (i=1; i<= nlstate ; i ++) {    
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      p2[thetai]=x[thetai]+delti[thetai]/k;
   else fprintf(ficgp," \%%*lf (\%%*lf)");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 }        k2=func(p2)-fx;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    
 #ifdef unix      p2[thetai]=x[thetai]-delti[thetai]/k;
 fprintf(ficgp,"\nset ter gif small size 400,300");      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 #endif      k3=func(p2)-fx;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    
    }      p2[thetai]=x[thetai]-delti[thetai]/k;
   }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   /*2 eme*/      k4=func(p2)-fx;
       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   for (k1=1; k1<= m ; k1 ++) {  #ifdef DEBUG
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);      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(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);
     for (i=1; i<= nlstate+1 ; i ++) {  #endif
       k=2*i;    }
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    return res;
       for (j=1; j<= nlstate+1 ; j ++) {  }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  /************** Inverse of matrix **************/
 }    void ludcmp(double **a, int n, int *indx, double *d) 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");  { 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    int i,imax,j,k; 
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    double big,dum,sum,temp; 
       for (j=1; j<= nlstate+1 ; j ++) {    double *vv; 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");   
         else fprintf(ficgp," \%%*lf (\%%*lf)");    vv=vector(1,n); 
 }      *d=1.0; 
       fprintf(ficgp,"\" t\"\" w l 0,");    for (i=1;i<=n;i++) { 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      big=0.0; 
       for (j=1; j<= nlstate+1 ; j ++) {      for (j=1;j<=n;j++) 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        if ((temp=fabs(a[i][j])) > big) big=temp; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 }        vv[i]=1.0/big; 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    } 
       else fprintf(ficgp,"\" t\"\" w l 0,");    for (j=1;j<=n;j++) { 
     }      for (i=1;i<j;i++) { 
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        sum=a[i][j]; 
   }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
          a[i][j]=sum; 
   /*3eme*/      } 
       big=0.0; 
   for (k1=1; k1<= m ; k1 ++) {      for (i=j;i<=n;i++) { 
     for (cpt=1; cpt<= nlstate ; cpt ++) {        sum=a[i][j]; 
       k=2+nlstate*(cpt-1);        for (k=1;k<j;k++) 
       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",agemin,fage,fileres,k1-1,k1-1,k,cpt);          sum -= a[i][k]*a[k][j]; 
       for (i=1; i< nlstate ; i ++) {        a[i][j]=sum; 
         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);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       }          big=dum; 
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          imax=i; 
     }        } 
     }      } 
        if (j != imax) { 
   /* CV preval stat */        for (k=1;k<=n;k++) { 
     for (k1=1; k1<= m ; k1 ++) {          dum=a[imax][k]; 
     for (cpt=1; cpt<nlstate ; cpt ++) {          a[imax][k]=a[j][k]; 
       k=3;          a[j][k]=dum; 
       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/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);        } 
         *d = -(*d); 
       for (i=1; i< nlstate ; i ++)        vv[imax]=vv[j]; 
         fprintf(ficgp,"+$%d",k+i+1);      } 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      indx[j]=imax; 
            if (a[j][j] == 0.0) a[j][j]=TINY; 
       l=3+(nlstate+ndeath)*cpt;      if (j != n) { 
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        dum=1.0/(a[j][j]); 
       for (i=1; i< nlstate ; i ++) {        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         l=3+(nlstate+ndeath)*cpt;      } 
         fprintf(ficgp,"+$%d",l+i+1);    } 
       }    free_vector(vv,1,n);  /* Doesn't work */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    ;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  } 
     }  
   }    void lubksb(double **a, int n, int *indx, double b[]) 
    { 
   /* proba elementaires */    int i,ii=0,ip,j; 
    for(i=1,jk=1; i <=nlstate; i++){    double sum; 
     for(k=1; k <=(nlstate+ndeath); k++){   
       if (k != i) {    for (i=1;i<=n;i++) { 
         for(j=1; j <=ncovmodel; j++){      ip=indx[i]; 
              sum=b[ip]; 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      b[ip]=b[i]; 
           jk++;      if (ii) 
           fprintf(ficgp,"\n");        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
         }      else if (sum) ii=i; 
       }      b[i]=sum; 
     }    } 
     }    for (i=n;i>=1;i--) { 
       sum=b[i]; 
     for(jk=1; jk <=m; jk++) {      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);      b[i]=sum/a[i][i]; 
    i=1;    } 
    for(k2=1; k2<=nlstate; k2++) {  } 
      k3=i;  
      for(k=1; k<=(nlstate+ndeath); k++) {  void pstamp(FILE *fichier)
        if (k != k2){  {
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
 ij=1;  }
         for(j=3; j <=ncovmodel; j++) {  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  /************ Frequencies ********************/
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  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[])
             ij++;  {  /* Some frequencies */
           }    
           else    int i, m, jk, k1,i1, j1, bool, z1,j;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    int first;
         }    double ***freq; /* Frequencies */
           fprintf(ficgp,")/(1");    double *pp, **prop;
            double pos,posprop, k2, dateintsum=0,k2cpt=0;
         for(k1=1; k1 <=nlstate; k1++){      char fileresp[FILENAMELENGTH];
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    
 ij=1;    pp=vector(1,nlstate);
           for(j=3; j <=ncovmodel; j++){    prop=matrix(1,nlstate,iagemin,iagemax+3);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    strcpy(fileresp,"p");
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    strcat(fileresp,fileres);
             ij++;    if((ficresp=fopen(fileresp,"w"))==NULL) {
           }      printf("Problem with prevalence resultfile: %s\n", fileresp);
           else      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      exit(0);
           }    }
           fprintf(ficgp,")");    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
         }    j1=0;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    j=cptcoveff;
         i=i+ncovmodel;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
        }  
      }    first=1;
    }  
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    for(k1=1; k1<=j;k1++){
    }      for(i1=1; i1<=ncodemax[k1];i1++){
            j1++;
   fclose(ficgp);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
 }  /* end gnuplot */          scanf("%d", i);*/
         for (i=-5; i<=nlstate+ndeath; i++)  
           for (jk=-5; jk<=nlstate+ndeath; jk++)  
 /*************** Moving average **************/            for(m=iagemin; m <= iagemax+3; m++)
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){              freq[i][jk][m]=0;
   
   int i, cpt, cptcod;      for (i=1; i<=nlstate; i++)  
     for (agedeb=agemin; agedeb<=fage; agedeb++)        for(m=iagemin; m <= iagemax+3; m++)
       for (i=1; i<=nlstate;i++)          prop[i][m]=0;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        
           mobaverage[(int)agedeb][i][cptcod]=0.;        dateintsum=0;
            k2cpt=0;
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){        for (i=1; i<=imx; i++) {
       for (i=1; i<=nlstate;i++){          bool=1;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          if  (cptcovn>0) {
           for (cpt=0;cpt<=4;cpt++){            for (z1=1; z1<=cptcoveff; z1++) 
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           }                bool=0;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          }
         }          if (bool==1){
       }            for(m=firstpass; m<=lastpass; m++){
     }              k2=anint[m][i]+(mint[m][i]/12.);
                  /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
 }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
 /************** Forecasting ******************/                if (m<lastpass) {
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){                  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];
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                }
   int *popage;                
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   double *popeffectif,*popcount;                  dateintsum=dateintsum+k2;
   double ***p3mat;                  k2cpt++;
   char fileresf[FILENAMELENGTH];                }
                 /*}*/
  agelim=AGESUP;            }
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          }
         }
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);         
          /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
          pstamp(ficresp);
   strcpy(fileresf,"f");        if  (cptcovn>0) {
   strcat(fileresf,fileres);          fprintf(ficresp, "\n#********** Variable "); 
   if((ficresf=fopen(fileresf,"w"))==NULL) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     printf("Problem with forecast resultfile: %s\n", fileresf);          fprintf(ficresp, "**********\n#");
   }        }
   printf("Computing forecasting: result on file '%s' \n", fileresf);        for(i=1; i<=nlstate;i++) 
           fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        fprintf(ficresp, "\n");
         
   if (mobilav==1) {        for(i=iagemin; i <= iagemax+3; i++){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          if(i==iagemax+3){
     movingaverage(agedeb, fage, agemin, mobaverage);            fprintf(ficlog,"Total");
   }          }else{
             if(first==1){
   stepsize=(int) (stepm+YEARM-1)/YEARM;              first=0;
   if (stepm<=12) stepsize=1;              printf("See log file for details...\n");
              }
   agelim=AGESUP;            fprintf(ficlog,"Age %d", i);
            }
   hstepm=1;          for(jk=1; jk <=nlstate ; jk++){
   hstepm=hstepm/stepm;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   yp1=modf(dateintmean,&yp);              pp[jk] += freq[jk][m][i]; 
   anprojmean=yp;          }
   yp2=modf((yp1*12),&yp);          for(jk=1; jk <=nlstate ; jk++){
   mprojmean=yp;            for(m=-1, pos=0; m <=0 ; m++)
   yp1=modf((yp2*30.5),&yp);              pos += freq[jk][m][i];
   jprojmean=yp;            if(pp[jk]>=1.e-10){
   if(jprojmean==0) jprojmean=1;              if(first==1){
   if(mprojmean==0) jprojmean=1;                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                }
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
              }else{
   for(cptcov=1;cptcov<=i2;cptcov++){              if(first==1)
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       k=k+1;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       fprintf(ficresf,"\n#******");            }
       for(j=1;j<=cptcoveff;j++) {          }
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }          for(jk=1; jk <=nlstate ; jk++){
       fprintf(ficresf,"******\n");            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       fprintf(ficresf,"# StartingAge FinalAge");              pp[jk] += freq[jk][m][i];
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);          }       
                for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
                  pos += pp[jk];
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {            posprop += prop[jk][i];
         fprintf(ficresf,"\n");          }
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){              if(first==1)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
           nhstepm = nhstepm/hstepm;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                      }else{
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              if(first==1)
           oldm=oldms;savm=savms;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                    }
           for (h=0; h<=nhstepm; h++){            if( i <= iagemax){
             if (h==(int) (calagedate+YEARM*cpt)) {              if(pos>=1.e-5){
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
             }                /*probs[i][jk][j1]= pp[jk]/pos;*/
             for(j=1; j<=nlstate+ndeath;j++) {                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
               kk1=0.;kk2=0;              }
               for(i=1; i<=nlstate;i++) {                            else
                 if (mobilav==1)                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];            }
                 else {          }
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          
                 }          for(jk=-1; jk <=nlstate+ndeath; jk++)
                            for(m=-1; m <=nlstate+ndeath; m++)
               }              if(freq[jk][m][i] !=0 ) {
               if (h==(int)(calagedate+12*cpt)){              if(first==1)
                 fprintf(ficresf," %.3f", kk1);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                                        fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }              }
             }          if(i <= iagemax)
           }            fprintf(ficresp,"\n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if(first==1)
         }            printf("Others in log...\n");
       }          fprintf(ficlog,"\n");
     }        }
   }      }
            }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    dateintmean=dateintsum/k2cpt; 
    
   fclose(ficresf);    fclose(ficresp);
 }    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
 /************** Forecasting ******************/    free_vector(pp,1,nlstate);
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
      /* End of Freq */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  }
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  /************ Prevalence ********************/
   double *popeffectif,*popcount;  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)
   double ***p3mat,***tabpop,***tabpopprev;  {  
   char filerespop[FILENAMELENGTH];    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       We still use firstpass and lastpass as another selection.
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    */
   agelim=AGESUP;   
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    int i, m, jk, k1, i1, j1, bool, z1,j;
      double ***freq; /* Frequencies */
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    double *pp, **prop;
      double pos,posprop; 
      double  y2; /* in fractional years */
   strcpy(filerespop,"pop");    int iagemin, iagemax;
   strcat(filerespop,fileres);  
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    iagemin= (int) agemin;
     printf("Problem with forecast resultfile: %s\n", filerespop);    iagemax= (int) agemax;
   }    /*pp=vector(1,nlstate);*/
   printf("Computing forecasting: result on file '%s' \n", filerespop);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    j1=0;
     
   if (mobilav==1) {    j=cptcoveff;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     movingaverage(agedeb, fage, agemin, mobaverage);    
   }    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;        j1++;
   if (stepm<=12) stepsize=1;        
          for (i=1; i<=nlstate; i++)  
   agelim=AGESUP;          for(m=iagemin; m <= iagemax+3; m++)
              prop[i][m]=0.0;
   hstepm=1;       
   hstepm=hstepm/stepm;        for (i=1; i<=imx; i++) { /* Each individual */
            bool=1;
   if (popforecast==1) {          if  (cptcovn>0) {
     if((ficpop=fopen(popfile,"r"))==NULL) {            for (z1=1; z1<=cptcoveff; z1++) 
       printf("Problem with population file : %s\n",popfile);exit(0);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     }                bool=0;
     popage=ivector(0,AGESUP);          } 
     popeffectif=vector(0,AGESUP);          if (bool==1) { 
     popcount=vector(0,AGESUP);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
                  y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     i=1;                if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                    if(agev[m][i]==1) agev[m][i]=iagemax+2;
     imx=i;                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   }                  /*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];
   for(cptcov=1;cptcov<=i2;cptcov++){                  prop[s[m][i]][iagemax+3] += weight[i]; 
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                } 
       k=k+1;              }
       fprintf(ficrespop,"\n#******");            } /* end selection of waves */
       for(j=1;j<=cptcoveff;j++) {          }
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }
       }        for(i=iagemin; i <= iagemax+3; i++){  
       fprintf(ficrespop,"******\n");          
       fprintf(ficrespop,"# Age");          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);            posprop += prop[jk][i]; 
       if (popforecast==1)  fprintf(ficrespop," [Population]");          } 
        
       for (cpt=0; cpt<=0;cpt++) {          for(jk=1; jk <=nlstate ; jk++){     
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);              if( i <=  iagemax){ 
                      if(posprop>=1.e-5){ 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){                probs[i][jk][j1]= prop[jk][i]/posprop;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              } else
           nhstepm = nhstepm/hstepm;                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
                      } 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }/* end jk */ 
           oldm=oldms;savm=savms;        }/* end i */ 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        } /* end i1 */
            } /* end k1 */
           for (h=0; h<=nhstepm; h++){    
             if (h==(int) (calagedate+YEARM*cpt)) {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    /*free_vector(pp,1,nlstate);*/
             }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
             for(j=1; j<=nlstate+ndeath;j++) {  }  /* End of prevalence */
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                /************* Waves Concatenation ***************/
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  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)
                 else {  {
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    /* 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
               if (h==(int)(calagedate+12*cpt)){       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;       and mw[mi+1][i]. dh depends on stepm.
                   /*fprintf(ficrespop," %.3f", kk1);       */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  
               }    int i, mi, m;
             }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
             for(i=1; i<=nlstate;i++){       double sum=0., jmean=0.;*/
               kk1=0.;    int first;
                 for(j=1; j<=nlstate;j++){    int j, k=0,jk, ju, jl;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    double sum=0.;
                 }    first=0;
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    jmin=1e+5;
             }    jmax=-1;
     jmean=0.;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    for(i=1; i<=imx; i++){
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      mi=0;
           }      m=firstpass;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      while(s[m][i] <= nlstate){
         }        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       }          mw[++mi][i]=m;
          if(m >=lastpass)
   /******/          break;
         else
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {          m++;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        }/* end while */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){      if (s[m][i] > nlstate){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        mi++;     /* Death is another wave */
           nhstepm = nhstepm/hstepm;        /* if(mi==0)  never been interviewed correctly before death */
                     /* Only death is a correct wave */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        mw[mi][i]=m;
           oldm=oldms;savm=savms;      }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           for (h=0; h<=nhstepm; h++){      wav[i]=mi;
             if (h==(int) (calagedate+YEARM*cpt)) {      if(mi==0){
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        nbwarn++;
             }        if(first==0){
             for(j=1; j<=nlstate+ndeath;j++) {          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
               kk1=0.;kk2=0;          first=1;
               for(i=1; i<=nlstate;i++) {                      }
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];            if(first==1){
               }          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);        }
             }      } /* end mi==0 */
           }    } /* End individuals */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }    for(i=1; i<=imx; i++){
       }      for(mi=1; mi<wav[i];mi++){
    }        if (stepm <=0)
   }          dh[mi][i]=1;
          else{
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             if (agedc[i] < 2*AGESUP) {
   if (popforecast==1) {              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     free_ivector(popage,0,AGESUP);              if(j==0) j=1;  /* Survives at least one month after exam */
     free_vector(popeffectif,0,AGESUP);              else if(j<0){
     free_vector(popcount,0,AGESUP);                nberr++;
   }                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                j=1; /* Temporary Dangerous patch */
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                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);
   fclose(ficrespop);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
 }                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               }
 /***********************************************/              k=k+1;
 /**************** Main Program *****************/              if (j >= jmax){
 /***********************************************/                jmax=j;
                 ijmax=i;
 int main(int argc, char *argv[])              }
 {              if (j <= jmin){
                 jmin=j;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;                ijmin=i;
   double agedeb, agefin,hf;              }
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;              sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   double fret;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   double **xi,tmp,delta;            }
           }
   double dum; /* Dummy variable */          else{
   double ***p3mat;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   int *indx;  /*        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]); */
   char line[MAXLINE], linepar[MAXLINE];  
   char title[MAXLINE];            k=k+1;
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];            if (j >= jmax) {
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];              jmax=j;
                ijmax=i;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];            }
             else if (j <= jmin){
   char filerest[FILENAMELENGTH];              jmin=j;
   char fileregp[FILENAMELENGTH];              ijmin=i;
   char popfile[FILENAMELENGTH];            }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   int firstobs=1, lastobs=10;            /*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]);*/
   int sdeb, sfin; /* Status at beginning and end */            if(j<0){
   int c,  h , cpt,l;              nberr++;
   int ju,jl, mi;              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]);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;              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]);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            }
   int mobilav=0,popforecast=0;            sum=sum+j;
   int hstepm, nhstepm;          }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;          jk= j/stepm;
           jl= j -jk*stepm;
   double bage, fage, age, agelim, agebase;          ju= j -(jk+1)*stepm;
   double ftolpl=FTOL;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   double **prlim;            if(jl==0){
   double *severity;              dh[mi][i]=jk;
   double ***param; /* Matrix of parameters */              bh[mi][i]=0;
   double  *p;            }else{ /* We want a negative bias in order to only have interpolation ie
   double **matcov; /* Matrix of covariance */                    * to avoid the price of an extra matrix product in likelihood */
   double ***delti3; /* Scale */              dh[mi][i]=jk+1;
   double *delti; /* Scale */              bh[mi][i]=ju;
   double ***eij, ***vareij;            }
   double **varpl; /* Variances of prevalence limits by age */          }else{
   double *epj, vepp;            if(jl <= -ju){
   double kk1, kk2;              dh[mi][i]=jk;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;              bh[mi][i]=jl;       /* bias is positive if real duration
                                     * is higher than the multiple of stepm and negative otherwise.
                                    */
   char version[80]="Imach version 0.71, February 2002, INED-EUROREVES ";            }
   char *alph[]={"a","a","b","c","d","e"}, str[4];            else{
               dh[mi][i]=jk+1;
               bh[mi][i]=ju;
   char z[1]="c", occ;            }
 #include <sys/time.h>            if(dh[mi][i]==0){
 #include <time.h>              dh[mi][i]=1; /* At least one step */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];              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);*/
   /* long total_usecs;            }
   struct timeval start_time, end_time;          } /* end if mle */
          }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      } /* end wave */
     }
     jmean=sum/k;
   printf("\n%s",version);    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);
   if(argc <=1){    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);
     printf("\nEnter the parameter file name: ");   }
     scanf("%s",pathtot);  
   }  /*********** Tricode ****************************/
   else{  void tricode(int *Tvar, int **nbcode, int imx)
     strcpy(pathtot,argv[1]);  {
   }    /* Uses cptcovn+2*cptcovprod as the number of covariates */
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
   /*cygwin_split_path(pathtot,path,optionfile);  
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   /* cutv(path,optionfile,pathtot,'\\');*/    int modmaxcovj=0; /* Modality max of covariates j */
     cptcoveff=0; 
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);   
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    for (k=0; k<maxncov; k++) Ndum[k]=0;
   chdir(path);    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
   replace(pathc,path);  
     for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
 /*-------- arguments in the command line --------*/      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the 
                                  modality of this covariate Vj*/ 
   strcpy(fileres,"r");        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
   strcat(fileres, optionfilefiname);                                        modality of the nth covariate of individual i. */
   strcat(fileres,".txt");    /* Other files have txt extension */        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   /*---------arguments file --------*/        if (ij > modmaxcovj) modmaxcovj=ij; 
         /* getting the maximum value of the modality of the covariate
   if((ficpar=fopen(optionfile,"r"))==NULL)    {           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
     printf("Problem with optionfile %s\n",optionfile);           female is 1, then modmaxcovj=1.*/
     goto end;      }
   }  
       for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*/
   strcpy(filereso,"o");        if( Ndum[i] != 0 )
   strcat(filereso,fileres);          ncodemax[j]++; 
   if((ficparo=fopen(filereso,"w"))==NULL) {        /* Number of modalities of the j th covariate. In fact
     printf("Problem with Output resultfile: %s\n", filereso);goto end;           ncodemax[j]=2 (dichotom. variables only) but it could be more for
   }           historical reasons */
       } /* Ndum[-1] number of undefined modalities */
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
     ungetc(c,ficpar);      ij=1; 
     fgets(line, MAXLINE, ficpar);      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
     puts(line);        for (k=0; k<= maxncov; k++) { /* k=-1 ? NCOVMAX*/
     fputs(line,ficparo);          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
   }            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
   ungetc(c,ficpar);                                       k is a modality. If we have model=V1+V1*sex 
                                        then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);            ij++;
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);          }
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);          if (ij > ncodemax[j]) break; 
 while((c=getc(ficpar))=='#' && c!= EOF){        }  
     ungetc(c,ficpar);      } 
     fgets(line, MAXLINE, ficpar);    }  
     puts(line);  
     fputs(line,ficparo);   for (k=0; k< maxncov; k++) Ndum[k]=0;
   }  
   ungetc(c,ficpar);   for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
       /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
         ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
   covar=matrix(0,NCOVMAX,1,n);     Ndum[ij]++;
   cptcovn=0;   }
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  
    ij=1;
   ncovmodel=2+cptcovn;   for (i=1; i<= maxncov; i++) {
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */     if((Ndum[i]!=0) && (i<=ncovcol)){
         Tvaraff[ij]=i; /*For printing */
   /* Read guess parameters */       ij++;
   /* Reads comments: lines beginning with '#' */     }
   while((c=getc(ficpar))=='#' && c!= EOF){   }
     ungetc(c,ficpar);   ij--;
     fgets(line, MAXLINE, ficpar);   cptcoveff=ij; /*Number of simple covariates*/
     puts(line);  }
     fputs(line,ficparo);  
   }  /*********** Health Expectancies ****************/
   ungetc(c,ficpar);  
    void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
     for(i=1; i <=nlstate; i++)  {
     for(j=1; j <=nlstate+ndeath-1; j++){    /* Health expectancies, no variances */
       fscanf(ficpar,"%1d%1d",&i1,&j1);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
       fprintf(ficparo,"%1d%1d",i1,j1);    int nhstepma, nstepma; /* Decreasing with age */
       printf("%1d%1d",i,j);    double age, agelim, hf;
       for(k=1; k<=ncovmodel;k++){    double ***p3mat;
         fscanf(ficpar," %lf",&param[i][j][k]);    double eip;
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);    pstamp(ficreseij);
       }    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
       fscanf(ficpar,"\n");    fprintf(ficreseij,"# Age");
       printf("\n");    for(i=1; i<=nlstate;i++){
       fprintf(ficparo,"\n");      for(j=1; j<=nlstate;j++){
     }        fprintf(ficreseij," e%1d%1d ",i,j);
        }
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      fprintf(ficreseij," e%1d. ",i);
     }
   p=param[1][1];    fprintf(ficreseij,"\n");
    
   /* Reads comments: lines beginning with '#' */    
   while((c=getc(ficpar))=='#' && c!= EOF){    if(estepm < stepm){
     ungetc(c,ficpar);      printf ("Problem %d lower than %d\n",estepm, stepm);
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    else  hstepm=estepm;   
     fputs(line,ficparo);    /* We compute the life expectancy from trapezoids spaced every estepm months
   }     * This is mainly to measure the difference between two models: for example
   ungetc(c,ficpar);     * 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 
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);     * progression in between and thus overestimating or underestimating according
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */     * to the curvature of the survival function. If, for the same date, we 
   for(i=1; i <=nlstate; i++){     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     for(j=1; j <=nlstate+ndeath-1; j++){     * to compare the new estimate of Life expectancy with the same linear 
       fscanf(ficpar,"%1d%1d",&i1,&j1);     * hypothesis. A more precise result, taking into account a more precise
       printf("%1d%1d",i,j);     * curvature will be obtained if estepm is as small as stepm. */
       fprintf(ficparo,"%1d%1d",i1,j1);  
       for(k=1; k<=ncovmodel;k++){    /* For example we decided to compute the life expectancy with the smallest unit */
         fscanf(ficpar,"%le",&delti3[i][j][k]);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         printf(" %le",delti3[i][j][k]);       nhstepm is the number of hstepm from age to agelim 
         fprintf(ficparo," %le",delti3[i][j][k]);       nstepm is the number of stepm from age to agelin. 
       }       Look at hpijx to understand the reason of that which relies in memory size
       fscanf(ficpar,"\n");       and note for a fixed period like estepm months */
       printf("\n");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       fprintf(ficparo,"\n");       survival function given by stepm (the optimization length). Unfortunately it
     }       means that if the survival funtion is printed only each two years of age and if
   }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   delti=delti3[1][1];       results. So we changed our mind and took the option of the best precision.
      */
   /* Reads comments: lines beginning with '#' */    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    agelim=AGESUP;
     fgets(line, MAXLINE, ficpar);    /* If stepm=6 months */
     puts(line);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     fputs(line,ficparo);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   }      
   ungetc(c,ficpar);  /* nhstepm age range expressed in number of stepm */
      nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   matcov=matrix(1,npar,1,npar);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   for(i=1; i <=npar; i++){    /* if (stepm >= YEARM) hstepm=1;*/
     fscanf(ficpar,"%s",&str);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     printf("%s",str);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fprintf(ficparo,"%s",str);  
     for(j=1; j <=i; j++){    for (age=bage; age<=fage; age ++){ 
       fscanf(ficpar," %le",&matcov[i][j]);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       printf(" %.5le",matcov[i][j]);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       fprintf(ficparo," %.5le",matcov[i][j]);      /* if (stepm >= YEARM) hstepm=1;*/
     }      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     fscanf(ficpar,"\n");  
     printf("\n");      /* If stepm=6 months */
     fprintf(ficparo,"\n");      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   }         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   for(i=1; i <=npar; i++)      
     for(j=i+1;j<=npar;j++)      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       matcov[i][j]=matcov[j][i];      
          hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   printf("\n");      
       printf("%d|",(int)age);fflush(stdout);
       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     /*-------- Rewriting paramater file ----------*/      
      strcpy(rfileres,"r");    /* "Rparameterfile */      /* Computing expectancies */
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/      for(i=1; i<=nlstate;i++)
      strcat(rfileres,".");    /* */        for(j=1; j<=nlstate;j++)
      strcat(rfileres,optionfilext);    /* Other files have txt extension */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     if((ficres =fopen(rfileres,"w"))==NULL) {            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       printf("Problem writing new parameter file: %s\n", fileres);goto end;            
     }            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     fprintf(ficres,"#%s\n",version);  
              }
     /*-------- data file ----------*/  
     if((fic=fopen(datafile,"r"))==NULL)    {      fprintf(ficreseij,"%3.0f",age );
       printf("Problem with datafile: %s\n", datafile);goto end;      for(i=1; i<=nlstate;i++){
     }        eip=0;
         for(j=1; j<=nlstate;j++){
     n= lastobs;          eip +=eij[i][j][(int)age];
     severity = vector(1,maxwav);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
     outcome=imatrix(1,maxwav+1,1,n);        }
     num=ivector(1,n);        fprintf(ficreseij,"%9.4f", eip );
     moisnais=vector(1,n);      }
     annais=vector(1,n);      fprintf(ficreseij,"\n");
     moisdc=vector(1,n);      
     andc=vector(1,n);    }
     agedc=vector(1,n);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     cod=ivector(1,n);    printf("\n");
     weight=vector(1,n);    fprintf(ficlog,"\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);  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[] )
     adl=imatrix(1,maxwav+1,1,n);      
     tab=ivector(1,NCOVMAX);  {
     ncodemax=ivector(1,8);    /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .
     i=1;    */
     while (fgets(line, MAXLINE, fic) != NULL)    {    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
       if ((i >= firstobs) && (i <=lastobs)) {    int nhstepma, nstepma; /* Decreasing with age */
            double age, agelim, hf;
         for (j=maxwav;j>=1;j--){    double ***p3matp, ***p3matm, ***varhe;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    double **dnewm,**doldm;
           strcpy(line,stra);    double *xp, *xm;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double **gp, **gm;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double ***gradg, ***trgradg;
         }    int theta;
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    double eip, vip;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    xp=vector(1,npar);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    xm=vector(1,npar);
     dnewm=matrix(1,nlstate*nlstate,1,npar);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
         for (j=ncov;j>=1;j--){    
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    pstamp(ficresstdeij);
         }    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
         num[i]=atol(stra);    fprintf(ficresstdeij,"# Age");
            for(i=1; i<=nlstate;i++){
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){      for(j=1; j<=nlstate;j++)
           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;}*/        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       fprintf(ficresstdeij," e%1d. ",i);
         i=i+1;    }
       }    fprintf(ficresstdeij,"\n");
     }  
     /* printf("ii=%d", ij);    pstamp(ficrescveij);
        scanf("%d",i);*/    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   imx=i-1; /* Number of individuals */    fprintf(ficrescveij,"# Age");
     for(i=1; i<=nlstate;i++)
   /* for (i=1; i<=imx; i++){      for(j=1; j<=nlstate;j++){
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        cptj= (j-1)*nlstate+i;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;        for(i2=1; i2<=nlstate;i2++)
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          for(j2=1; j2<=nlstate;j2++){
     }            cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
     for (i=1; i<=imx; i++)              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
     if (covar[1][i]==0) 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]));*/          }
       }
   /* Calculation of the number of parameter from char model*/    fprintf(ficrescveij,"\n");
   Tvar=ivector(1,15);    
   Tprod=ivector(1,15);    if(estepm < stepm){
   Tvaraff=ivector(1,15);      printf ("Problem %d lower than %d\n",estepm, stepm);
   Tvard=imatrix(1,15,1,2);    }
   Tage=ivector(1,15);          else  hstepm=estepm;   
        /* We compute the life expectancy from trapezoids spaced every estepm months
   if (strlen(model) >1){     * This is mainly to measure the difference between two models: for example
     j=0, j1=0, k1=1, k2=1;     * if stepm=24 months pijx are given only every 2 years and by summing them
     j=nbocc(model,'+');     * we are calculating an estimate of the Life Expectancy assuming a linear 
     j1=nbocc(model,'*');     * progression in between and thus overestimating or underestimating according
     cptcovn=j+1;     * to the curvature of the survival function. If, for the same date, we 
     cptcovprod=j1;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         * to compare the new estimate of Life expectancy with the same linear 
         * hypothesis. A more precise result, taking into account a more precise
     strcpy(modelsav,model);     * curvature will be obtained if estepm is as small as stepm. */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  
       printf("Error. Non available option model=%s ",model);    /* For example we decided to compute the life expectancy with the smallest unit */
       goto end;    /* 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. 
     for(i=(j+1); i>=1;i--){       Look at hpijx to understand the reason of that which relies in memory size
       cutv(stra,strb,modelsav,'+');       and note for a fixed period like estepm months */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/       survival function given by stepm (the optimization length). Unfortunately it
       /*scanf("%d",i);*/       means that if the survival funtion is printed only each two years of age and if
       if (strchr(strb,'*')) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         cutv(strd,strc,strb,'*');       results. So we changed our mind and took the option of the best precision.
         if (strcmp(strc,"age")==0) {    */
           cptcovprod--;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           cutv(strb,stre,strd,'V');  
           Tvar[i]=atoi(stre);    /* If stepm=6 months */
           cptcovage++;    /* nhstepm age range expressed in number of stepm */
             Tage[cptcovage]=i;    agelim=AGESUP;
             /*printf("stre=%s ", stre);*/    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
         }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         else if (strcmp(strd,"age")==0) {    /* if (stepm >= YEARM) hstepm=1;*/
           cptcovprod--;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           cutv(strb,stre,strc,'V');    
           Tvar[i]=atoi(stre);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           cptcovage++;    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           Tage[cptcovage]=i;    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
         }    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
         else {    gp=matrix(0,nhstepm,1,nlstate*nlstate);
           cutv(strb,stre,strc,'V');    gm=matrix(0,nhstepm,1,nlstate*nlstate);
           Tvar[i]=ncov+k1;  
           cutv(strb,strc,strd,'V');    for (age=bage; age<=fage; age ++){ 
           Tprod[k1]=i;      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
           Tvard[k1][1]=atoi(strc);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           Tvard[k1][2]=atoi(stre);      /* if (stepm >= YEARM) hstepm=1;*/
           Tvar[cptcovn+k2]=Tvard[k1][1];      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  
           for (k=1; k<=lastobs;k++)      /* If stepm=6 months */
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      /* Computed by stepm unit matrices, product of hstepma matrices, stored
           k1++;         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           k2=k2+2;      
         }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       }  
       else {      /* Computing  Variances of health expectancies */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
        /*  scanf("%d",i);*/         decrease memory allocation */
       cutv(strd,strc,strb,'V');      for(theta=1; theta <=npar; theta++){
       Tvar[i]=atoi(strc);        for(i=1; i<=npar; i++){ 
       }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       strcpy(modelsav,stra);            xm[i] = x[i] - (i==theta ?delti[theta]:0);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        }
         scanf("%d",i);*/        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
     }        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
 }    
          for(j=1; j<= nlstate; j++){
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);          for(i=1; i<=nlstate; i++){
   printf("cptcovprod=%d ", cptcovprod);            for(h=0; h<=nhstepm-1; h++){
   scanf("%d ",i);*/              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
     fclose(fic);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             }
     /*  if(mle==1){*/          }
     if (weightopt != 1) { /* Maximisation without weights*/        }
       for(i=1;i<=n;i++) weight[i]=1.0;       
     }        for(ij=1; ij<= nlstate*nlstate; ij++)
     /*-calculation of age at interview from date of interview and age at death -*/          for(h=0; h<=nhstepm-1; h++){
     agev=matrix(1,maxwav,1,imx);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
    for (i=1; i<=imx; i++)      }/* End theta */
      for(m=2; (m<= maxwav); m++)      
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      
          anint[m][i]=9999;      for(h=0; h<=nhstepm-1; h++)
          s[m][i]=-1;        for(j=1; j<=nlstate*nlstate;j++)
        }          for(theta=1; theta <=npar; theta++)
                trgradg[h][j][theta]=gradg[h][theta][j];
     for (i=1; i<=imx; i++)  {      
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){       for(ij=1;ij<=nlstate*nlstate;ij++)
         if(s[m][i] >0){        for(ji=1;ji<=nlstate*nlstate;ji++)
           if (s[m][i] == nlstate+1) {          varhe[ij][ji][(int)age] =0.;
             if(agedc[i]>0)  
               if(moisdc[i]!=99 && andc[i]!=9999)       printf("%d|",(int)age);fflush(stdout);
               agev[m][i]=agedc[i];       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
             else {       for(h=0;h<=nhstepm-1;h++){
               if (andc[i]!=9999){        for(k=0;k<=nhstepm-1;k++){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
               agev[m][i]=-1;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
               }          for(ij=1;ij<=nlstate*nlstate;ij++)
             }            for(ji=1;ji<=nlstate*nlstate;ji++)
           }              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
           else if(s[m][i] !=9){ /* Should no more exist */        }
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      }
             if(mint[m][i]==99 || anint[m][i]==9999)  
               agev[m][i]=1;      /* Computing expectancies */
             else if(agev[m][i] <agemin){      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
               agemin=agev[m][i];      for(i=1; i<=nlstate;i++)
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/        for(j=1; j<=nlstate;j++)
             }          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             else if(agev[m][i] >agemax){            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
               agemax=agev[m][i];            
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/            /* 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]);*/
             }  
             /*agev[m][i]=anint[m][i]-annais[i];*/          }
             /*   agev[m][i] = age[i]+2*m;*/  
           }      fprintf(ficresstdeij,"%3.0f",age );
           else { /* =9 */      for(i=1; i<=nlstate;i++){
             agev[m][i]=1;        eip=0.;
             s[m][i]=-1;        vip=0.;
           }        for(j=1; j<=nlstate;j++){
         }          eip += eij[i][j][(int)age];
         else /*= 0 Unknown */          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
           agev[m][i]=1;            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
       }          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
            }
     }        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
     for (i=1; i<=imx; i++)  {      }
       for(m=1; (m<= maxwav); m++){      fprintf(ficresstdeij,"\n");
         if (s[m][i] > (nlstate+ndeath)) {  
           printf("Error: Wrong value in nlstate or ndeath\n");        fprintf(ficrescveij,"%3.0f",age );
           goto end;      for(i=1; i<=nlstate;i++)
         }        for(j=1; j<=nlstate;j++){
       }          cptj= (j-1)*nlstate+i;
     }          for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);              cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
     free_vector(severity,1,maxwav);                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
     free_imatrix(outcome,1,maxwav+1,1,n);            }
     free_vector(moisnais,1,n);        }
     free_vector(annais,1,n);      fprintf(ficrescveij,"\n");
     /* free_matrix(mint,1,maxwav,1,n);     
        free_matrix(anint,1,maxwav,1,n);*/    }
     free_vector(moisdc,1,n);    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_vector(andc,1,n);    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);
     wav=ivector(1,imx);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    printf("\n");
        fprintf(ficlog,"\n");
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
       Tcode=ivector(1,100);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
       ncodemax[1]=1;  }
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  
        /************ Variance ******************/
    codtab=imatrix(1,100,1,10);  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[])
    h=0;  {
    m=pow(2,cptcoveff);    /* Variance of health expectancies */
      /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
    for(k=1;k<=cptcoveff; k++){    /* double **newm;*/
      for(i=1; i <=(m/pow(2,k));i++){    double **dnewm,**doldm;
        for(j=1; j <= ncodemax[k]; j++){    double **dnewmp,**doldmp;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    int i, j, nhstepm, hstepm, h, nstepm ;
            h++;    int k, cptcode;
            if (h>m) h=1;codtab[h][k]=j;    double *xp;
          }    double **gp, **gm;  /* for var eij */
        }    double ***gradg, ***trgradg; /*for var eij */
      }    double **gradgp, **trgradgp; /* for var p point j */
    }    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
    /*for(i=1; i <=m ;i++){    double age,agelim, hf;
      for(k=1; k <=cptcovn; k++){    double ***mobaverage;
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);    int theta;
      }    char digit[4];
      printf("\n");    char digitp[25];
    }  
    scanf("%d",i);*/    char fileresprobmorprev[FILENAMELENGTH];
      
    /* Calculates basic frequencies. Computes observed prevalence at single age    if(popbased==1){
        and prints on file fileres'p'. */      if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
          else strcpy(digitp,"-populbased-nomobil-");
        }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    else 
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      strcpy(digitp,"-stablbased-");
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if (mobilav!=0) {
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
            if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     /* For Powell, parameters are in a vector p[] starting at p[1]        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      }
     }
     if(mle==1){  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    strcpy(fileresprobmorprev,"prmorprev"); 
     }    sprintf(digit,"%-d",ij);
        /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     /*--------- results files --------------*/    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
      strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
    jk=1;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
    fprintf(ficres,"# Parameters\n");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
    printf("# Parameters\n");    }
    for(i=1,jk=1; i <=nlstate; i++){    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      for(k=1; k <=(nlstate+ndeath); k++){   
        if (k != i)    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
          {    pstamp(ficresprobmorprev);
            printf("%d%d ",i,k);    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
            fprintf(ficres,"%1d%1d ",i,k);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
            for(j=1; j <=ncovmodel; j++){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
              printf("%f ",p[jk]);      fprintf(ficresprobmorprev," p.%-d SE",j);
              fprintf(ficres,"%f ",p[jk]);      for(i=1; i<=nlstate;i++)
              jk++;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
            }    }  
            printf("\n");    fprintf(ficresprobmorprev,"\n");
            fprintf(ficres,"\n");    fprintf(ficgp,"\n# Routine varevsij");
          }    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
      }    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
    }    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
  if(mle==1){  /*   } */
     /* Computing hessian and covariance matrix */    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     ftolhess=ftol; /* Usually correct */    pstamp(ficresvij);
     hesscov(matcov, p, npar, delti, ftolhess, func);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
  }    if(popbased==1)
     fprintf(ficres,"# Scales\n");      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);
     printf("# Scales\n");    else
      for(i=1,jk=1; i <=nlstate; i++){      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
       for(j=1; j <=nlstate+ndeath; j++){    fprintf(ficresvij,"# Age");
         if (j!=i) {    for(i=1; i<=nlstate;i++)
           fprintf(ficres,"%1d%1d",i,j);      for(j=1; j<=nlstate;j++)
           printf("%1d%1d",i,j);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
           for(k=1; k<=ncovmodel;k++){    fprintf(ficresvij,"\n");
             printf(" %.5e",delti[jk]);  
             fprintf(ficres," %.5e",delti[jk]);    xp=vector(1,npar);
             jk++;    dnewm=matrix(1,nlstate,1,npar);
           }    doldm=matrix(1,nlstate,1,nlstate);
           printf("\n");    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
           fprintf(ficres,"\n");    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         }  
       }    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
      }    gpp=vector(nlstate+1,nlstate+ndeath);
        gmp=vector(nlstate+1,nlstate+ndeath);
     k=1;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficres,"# Covariance\n");    
     printf("# Covariance\n");    if(estepm < stepm){
     for(i=1;i<=npar;i++){      printf ("Problem %d lower than %d\n",estepm, stepm);
       /*  if (k>nlstate) k=1;    }
       i1=(i-1)/(ncovmodel*nlstate)+1;    else  hstepm=estepm;   
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    /* For example we decided to compute the life expectancy with the smallest unit */
       printf("%s%d%d",alph[k],i1,tab[i]);*/    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       fprintf(ficres,"%3d",i);       nhstepm is the number of hstepm from age to agelim 
       printf("%3d",i);       nstepm is the number of stepm from age to agelin. 
       for(j=1; j<=i;j++){       Look at function hpijx to understand why (it is linked to memory size questions) */
         fprintf(ficres," %.5e",matcov[i][j]);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         printf(" %.5e",matcov[i][j]);       survival function given by stepm (the optimization length). Unfortunately it
       }       means that if the survival funtion is printed every two years of age and if
       fprintf(ficres,"\n");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       printf("\n");       results. So we changed our mind and took the option of the best precision.
       k++;    */
     }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
        agelim = AGESUP;
     while((c=getc(ficpar))=='#' && c!= EOF){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       ungetc(c,ficpar);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       fgets(line, MAXLINE, ficpar);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       puts(line);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fputs(line,ficparo);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     }      gp=matrix(0,nhstepm,1,nlstate);
     ungetc(c,ficpar);      gm=matrix(0,nhstepm,1,nlstate);
    
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);  
          for(theta=1; theta <=npar; theta++){
     if (fage <= 2) {        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       bage = agemin;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fage = agemaxpar;        }
     }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
            prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     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\n",agemin,agemaxpar,bage,fage);        if (popbased==1) {
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);          if(mobilav ==0){
              for(i=1; i<=nlstate;i++)
     while((c=getc(ficpar))=='#' && c!= EOF){              prlim[i][i]=probs[(int)age][i][ij];
     ungetc(c,ficpar);          }else{ /* mobilav */ 
     fgets(line, MAXLINE, ficpar);            for(i=1; i<=nlstate;i++)
     puts(line);              prlim[i][i]=mobaverage[(int)age][i][ij];
     fputs(line,ficparo);          }
   }        }
   ungetc(c,ficpar);    
          for(j=1; j<= nlstate; j++){
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);          for(h=0; h<=nhstepm; h++){
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
                }
   while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);        /* This for computing probability of death (h=1 means
     fgets(line, MAXLINE, ficpar);           computed over hstepm matrices product = hstepm*stepm months) 
     puts(line);           as a weighted average of prlim.
     fputs(line,ficparo);        */
   }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   ungetc(c,ficpar);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
              gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        /* end probability of death */
    dateprev2=anprev2+mprev2/12.+jprev2/365.;  
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   fscanf(ficpar,"pop_based=%d\n",&popbased);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   fprintf(ficparo,"pop_based=%d\n",popbased);          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   fprintf(ficres,"pop_based=%d\n",popbased);          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     
   while((c=getc(ficpar))=='#' && c!= EOF){        if (popbased==1) {
     ungetc(c,ficpar);          if(mobilav ==0){
     fgets(line, MAXLINE, ficpar);            for(i=1; i<=nlstate;i++)
     puts(line);              prlim[i][i]=probs[(int)age][i][ij];
     fputs(line,ficparo);          }else{ /* mobilav */ 
   }            for(i=1; i<=nlstate;i++)
   ungetc(c,ficpar);              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);        }
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
 while((c=getc(ficpar))=='#' && c!= EOF){              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);        }
     puts(line);        /* This for computing probability of death (h=1 means
     fputs(line,ficparo);           computed over hstepm matrices product = hstepm*stepm months) 
   }           as a weighted average of prlim.
   ungetc(c,ficpar);        */
         for(j=nlstate+1;j<=nlstate+ndeath;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);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        }    
         /* end probability of death */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
         for(j=1; j<= nlstate; j++) /* vareij */
 /*------------ gnuplot -------------*/          for(h=0; h<=nhstepm; h++){
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            }
 /*------------ free_vector  -------------*/  
  chdir(path);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
            gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
  free_ivector(wav,1,imx);        }
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        } /* End theta */
  free_ivector(num,1,n);  
  free_vector(agedc,1,n);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
  /*free_matrix(covar,1,NCOVMAX,1,n);*/  
  fclose(ficparo);      for(h=0; h<=nhstepm; h++) /* veij */
  fclose(ficres);        for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
 /*--------- index.htm --------*/            trgradg[h][j][theta]=gradg[h][theta][j];
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
            trgradgp[j][theta]=gradgp[theta][j];
   /*--------------- Prevalence limit --------------*/    
    
   strcpy(filerespl,"pl");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   strcat(filerespl,fileres);      for(i=1;i<=nlstate;i++)
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        for(j=1;j<=nlstate;j++)
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          vareij[i][j][(int)age] =0.;
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      for(h=0;h<=nhstepm;h++){
   fprintf(ficrespl,"#Prevalence limit\n");        for(k=0;k<=nhstepm;k++){
   fprintf(ficrespl,"#Age ");          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   fprintf(ficrespl,"\n");          for(i=1;i<=nlstate;i++)
              for(j=1;j<=nlstate;j++)
   prlim=matrix(1,nlstate,1,nlstate);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   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 */      /* pptj */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   k=0;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   agebase=agemin;      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   agelim=agemaxpar;        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   ftolpl=1.e-10;          varppt[j][i]=doldmp[j][i];
   i1=cptcoveff;      /* end ppptj */
   if (cptcovn < 1){i1=1;}      /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   for(cptcov=1;cptcov<=i1;cptcov++){      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   
         k=k+1;      if (popbased==1) {
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        if(mobilav ==0){
         fprintf(ficrespl,"\n#******");          for(i=1; i<=nlstate;i++)
         for(j=1;j<=cptcoveff;j++)            prlim[i][i]=probs[(int)age][i][ij];
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }else{ /* mobilav */ 
         fprintf(ficrespl,"******\n");          for(i=1; i<=nlstate;i++)
                    prlim[i][i]=mobaverage[(int)age][i][ij];
         for (age=agebase; age<=agelim; age++){        }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      }
           fprintf(ficrespl,"%.0f",age );               
           for(i=1; i<=nlstate;i++)      /* This for computing probability of death (h=1 means
           fprintf(ficrespl," %.5f", prlim[i][i]);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           fprintf(ficrespl,"\n");         as a weighted average of prlim.
         }      */
       }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
     }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   fclose(ficrespl);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
   /*------------- h Pij x at various ages ------------*/      /* end probability of death */
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   }        for(i=1; i<=nlstate;i++){
   printf("Computing pij: result on file '%s' \n", filerespij);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
          }
   stepsize=(int) (stepm+YEARM-1)/YEARM;      } 
   /*if (stepm<=24) stepsize=2;*/      fprintf(ficresprobmorprev,"\n");
   
   agelim=AGESUP;      fprintf(ficresvij,"%.0f ",age );
   hstepm=stepsize*YEARM; /* Every year of age */      for(i=1; i<=nlstate;i++)
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */        for(j=1; j<=nlstate;j++){
            fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   k=0;        }
   for(cptcov=1;cptcov<=i1;cptcov++){      fprintf(ficresvij,"\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      free_matrix(gp,0,nhstepm,1,nlstate);
       k=k+1;      free_matrix(gm,0,nhstepm,1,nlstate);
         fprintf(ficrespij,"\n#****** ");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
         for(j=1;j<=cptcoveff;j++)      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrespij,"******\n");    } /* End age */
            free_vector(gpp,nlstate+1,nlstate+ndeath);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    free_vector(gmp,nlstate+1,nlstate+ndeath);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
           oldm=oldms;savm=savms;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
           fprintf(ficrespij,"# Age");  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
           for(i=1; i<=nlstate;i++)  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
             for(j=1; j<=nlstate+ndeath;j++)  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
               fprintf(ficrespij," %1d-%1d",i,j);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
           fprintf(ficrespij,"\n");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
           for (h=0; h<=nhstepm; h++){    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
             for(i=1; i<=nlstate;i++)    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);
               for(j=1; j<=nlstate+ndeath;j++)    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  */
             fprintf(ficrespij,"\n");  /*   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);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");    free_vector(xp,1,npar);
         }    free_matrix(doldm,1,nlstate,1,nlstate);
     }    free_matrix(dnewm,1,nlstate,1,npar);
   }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fclose(ficrespij);    fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   /*---------- Forecasting ------------------*/  }  /* end varevsij */
   if((stepm == 1) && (model==".")){  
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);  /************ Variance of prevlim ******************/
 if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  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[])
     free_matrix(mint,1,maxwav,1,n);  {
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    /* Variance of prevalence limit */
     free_vector(weight,1,n);}    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   else{    double **newm;
     erreur=108;    double **dnewm,**doldm;
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);    int i, j, nhstepm, hstepm;
   }    int k, cptcode;
      double *xp;
     double *gp, *gm;
   /*---------- Health expectancies and variances ------------*/    double **gradg, **trgradg;
     double age,agelim;
   strcpy(filerest,"t");    int theta;
   strcat(filerest,fileres);    
   if((ficrest=fopen(filerest,"w"))==NULL) {    pstamp(ficresvpl);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
   }    fprintf(ficresvpl,"# Age");
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   strcpy(filerese,"e");  
   strcat(filerese,fileres);    xp=vector(1,npar);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    dnewm=matrix(1,nlstate,1,npar);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    doldm=matrix(1,nlstate,1,nlstate);
   }    
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
  strcpy(fileresv,"v");    agelim = AGESUP;
   strcat(fileresv,fileres);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      if (stepm >= YEARM) hstepm=1;
   }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
   k=0;      gm=vector(1,nlstate);
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(theta=1; theta <=npar; theta++){
       k=k+1;        for(i=1; i<=npar; i++){ /* Computes gradient */
       fprintf(ficrest,"\n#****** ");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       for(j=1;j<=cptcoveff;j++)        }
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       fprintf(ficrest,"******\n");        for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       fprintf(ficreseij,"\n#****** ");      
       for(j=1;j<=cptcoveff;j++)        for(i=1; i<=npar; i++) /* Computes gradient */
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       fprintf(ficreseij,"******\n");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
       fprintf(ficresvij,"\n#****** ");          gm[i] = prlim[i][i];
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        for(i=1;i<=nlstate;i++)
       fprintf(ficresvij,"******\n");          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;      trgradg =matrix(1,nlstate,1,npar);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);    
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      for(j=1; j<=nlstate;j++)
       oldm=oldms;savm=savms;        for(theta=1; theta <=npar; theta++)
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          trgradg[j][theta]=gradg[theta][j];
      
       for(i=1;i<=nlstate;i++)
          varpl[i][(int)age] =0.;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       fprintf(ficrest,"\n");      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
       hf=1;  
       if (stepm >= YEARM) hf=stepm/YEARM;      fprintf(ficresvpl,"%.0f ",age );
       epj=vector(1,nlstate+1);      for(i=1; i<=nlstate;i++)
       for(age=bage; age <=fage ;age++){        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      fprintf(ficresvpl,"\n");
         if (popbased==1) {      free_vector(gp,1,nlstate);
           for(i=1; i<=nlstate;i++)      free_vector(gm,1,nlstate);
             prlim[i][i]=probs[(int)age][i][k];      free_matrix(gradg,1,npar,1,nlstate);
         }      free_matrix(trgradg,1,nlstate,1,npar);
            } /* End age */
         fprintf(ficrest," %.0f",age);  
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    free_vector(xp,1,npar);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    free_matrix(doldm,1,nlstate,1,npar);
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    free_matrix(dnewm,1,nlstate,1,nlstate);
           }  
           epj[nlstate+1] +=epj[j];  }
         }  
         for(i=1, vepp=0.;i <=nlstate;i++)  /************ Variance of one-step probabilities  ******************/
           for(j=1;j <=nlstate;j++)  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
             vepp += vareij[i][j][(int)age];  {
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    int i, j=0,  i1, k1, l1, t, tj;
         for(j=1;j <=nlstate;j++){    int k2, l2, j1,  z1;
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    int k=0,l, cptcode;
         }    int first=1, first1;
         fprintf(ficrest,"\n");    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
       }    double **dnewm,**doldm;
     }    double *xp;
   }    double *gp, *gm;
     double **gradg, **trgradg;
   fclose(ficreseij);    double **mu;
   fclose(ficresvij);    double age,agelim, cov[NCOVMAX];
   fclose(ficrest);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   fclose(ficpar);    int theta;
   free_vector(epj,1,nlstate+1);    char fileresprob[FILENAMELENGTH];
      char fileresprobcov[FILENAMELENGTH];
   /*------- Variance limit prevalence------*/      char fileresprobcor[FILENAMELENGTH];
   
   strcpy(fileresvpl,"vpl");    double ***varpij;
   strcat(fileresvpl,fileres);  
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    strcpy(fileresprob,"prob"); 
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    strcat(fileresprob,fileres);
     exit(0);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprob);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
   k=0;    strcpy(fileresprobcov,"probcov"); 
   for(cptcov=1;cptcov<=i1;cptcov++){    strcat(fileresprobcov,fileres);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       k=k+1;      printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficresvpl,"\n#****** ");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       for(j=1;j<=cptcoveff;j++)    }
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    strcpy(fileresprobcor,"probcor"); 
       fprintf(ficresvpl,"******\n");    strcat(fileresprobcor,fileres);
          if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       varpl=matrix(1,nlstate,(int) bage, (int) fage);      printf("Problem with resultfile: %s\n", fileresprobcor);
       oldm=oldms;savm=savms;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    }
     }    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
  }    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   fclose(ficresvpl);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   /*---------- End : free ----------------*/    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    pstamp(ficresprob);
      fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    fprintf(ficresprob,"# Age");
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    pstamp(ficresprobcov);
      fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
      fprintf(ficresprobcov,"# Age");
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    pstamp(ficresprobcor);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    fprintf(ficresprobcor,"# Age");
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);  
    
   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);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
   if(erreur >0)      }  
     printf("End of Imach with error %d\n",erreur);   /* fprintf(ficresprob,"\n");
   else   printf("End of Imach\n");    fprintf(ficresprobcov,"\n");
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    fprintf(ficresprobcor,"\n");
     */
   /* 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);*/    xp=vector(1,npar);
   /*printf("Total time was %d uSec.\n", total_usecs);*/    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   /*------ End -----------*/    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
  end:    first=1;
 #ifdef windows    fprintf(ficgp,"\n# Routine varprob");
   /* chdir(pathcd);*/    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
 #endif    fprintf(fichtm,"\n");
  /*system("wgnuplot graph.plt");*/  
  /*system("../gp37mgw/wgnuplot graph.plt");*/    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
  /*system("cd ../gp37mgw");*/    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    file %s<br>\n",optionfilehtmcov);
  strcpy(plotcmd,GNUPLOTPROGRAM);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
  strcat(plotcmd," ");  and drawn. It helps understanding how is the covariance between two incidences.\
  strcat(plotcmd,optionfilegnuplot);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
  system(plotcmd);    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
 #ifdef windows  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   while (z[0] != 'q') {  standard deviations wide on each axis. <br>\
     chdir(path);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
     printf("\nType e to edit output files, c to start again, and q for exiting: ");   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
     scanf("%s",z);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') {    cov[1]=1;
       chdir(path);    tj=cptcoveff;
       system(optionfilehtm);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     }    j1=0;
     else if (z[0] == 'q') exit(0);    for(t=1; t<=tj;t++){
   }      for(i1=1; i1<=ncodemax[t];i1++){ 
 #endif        j1++;
 }        if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;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++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             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.;
                     if ((lc2 <0) || (lc1 <0) ){
                       printf("Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);
                       lc1=fabs(lc1);
                       lc2=fabs(lc2);
                     }
   
                     /* 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;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     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]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+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);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* 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);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     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;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       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);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld 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);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld 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);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (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 birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  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 birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         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);
         return 1;
       }
       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);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           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);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   
   int decodemodel ( char model[], int lastobs)
   {
     int i, j, k;
     int i1, j1, k1, k2;
     char modelsav[80];
      char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     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*age+V3 =>(2 plus signs) + 1=3 
                     but the covariates which are product must be computed and stored. */
       cptcovprod=j1; /*Number of products  V1*V2 +v3*age = 2 */
       
       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);
         return 1;
       }
       
       /* 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 */
       /*    modelsav=V3*age+V2+V1+V4 strb=V3*age stra=V2+V1+V4 
           i=1 Tvar[1]=3 Tage[1]=1  
           i=2 Tvar[2]=2
           i=3 Tvar[3]=1
           i=4 Tvar[4]= 4
           i=5 Tvar[5]
         for (k=1; k<=cptcovn;k++) {
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
        */
       for(k=1; k<=(j+1);k++){
         cutv(strb,stra,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav=V3*age+V2+V1+V4 strb=V3*age stra=V2+V1+V4 
                                       */ 
         /* 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 V3*age+V2+V1+V4 strb=V3*age */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: strb=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'); /* stre="V3" */
             Tvar[k]=atoi(stre);  /* V1+V3*age+V2 Tvar[2]=3, and Tvar[3]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] =2 */
             /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           }
           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[k]=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]=k;  /* 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 (i=1; i<=lastobs;i++) /* Computes the new covariate which is a product of covar[n][i]* covar[m][i]
                                        and is stored at ncovol+k1 */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             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);*/
   
   
     return (0);
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     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);     
           return 1;
         }
       }
     }
   
     /*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); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     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];
     /*  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, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*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 ***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  *strt;*/
     char strtend[80];
   
     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 plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       cptcovn=nbocc(model,'+')+1;
     /* ncovprod */
     ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     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 */
   
   
     n= lastobs;
     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);
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* 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(decodemodel(model, lastobs) == 1)
       goto end;
   
       /*  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);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     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); 
   /*     ximort=gsl_matrix_alloc(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]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #elsedef
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       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);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #elsedef
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  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");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       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);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* 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.1.30  
changed lines
  Added in v.1.136


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