Diff for /imach/src/imach.c between versions 1.24 and 1.127

version 1.24, 2002/02/22 18:10:15 version 1.127, 2006/04/28 18:11:50
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.127  2006/04/28 18:11:50  brouard
      (Module): Yes the sum of survivors was wrong since
   This program computes Healthy Life Expectancies from    imach-114 because nhstepm was no more computed in the age
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    loop. Now we define nhstepma in the age loop.
   first survey ("cross") where individuals from different ages are    (Module): In order to speed up (in case of numerous covariates) we
   interviewed on their health status or degree of disability (in the    compute health expectancies (without variances) in a first step
   case of a health survey which is our main interest) -2- at least a    and then all the health expectancies with variances or standard
   second wave of interviews ("longitudinal") which measure each change    deviation (needs data from the Hessian matrices) which slows the
   (if any) in individual health status.  Health expectancies are    computation.
   computed from the time spent in each health state according to a    In the future we should be able to stop the program is only health
   model. More health states you consider, more time is necessary to reach the    expectancies and graph are needed without standard deviations.
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.126  2006/04/28 17:23:28  brouard
   probabibility to be observed in state j at the second wave    (Module): Yes the sum of survivors was wrong since
   conditional to be observed in state i at the first wave. Therefore    imach-114 because nhstepm was no more computed in the age
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    loop. Now we define nhstepma in the age loop.
   'age' is age and 'sex' is a covariate. If you want to have a more    Version 0.98h
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.125  2006/04/04 15:20:31  lievre
   you to do it.  More covariates you add, slower the    Errors in calculation of health expectancies. Age was not initialized.
   convergence.    Forecasting file added.
   
   The advantage of this computer programme, compared to a simple    Revision 1.124  2006/03/22 17:13:53  lievre
   multinomial logistic model, is clear when the delay between waves is not    Parameters are printed with %lf instead of %f (more numbers after the comma).
   identical for each individual. Also, if a individual missed an    The log-likelihood is printed in the log file
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      Revision 1.123  2006/03/20 10:52:43  brouard
     * imach.c (Module): <title> changed, corresponds to .htm file
   hPijx is the probability to be observed in state i at age x+h    name. <head> headers where missing.
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    * imach.c (Module): Weights can have a decimal point as for
   states. This elementary transition (by month or quarter trimester,    English (a comma might work with a correct LC_NUMERIC environment,
   semester or year) is model as a multinomial logistic.  The hPx    otherwise the weight is truncated).
   matrix is simply the matrix product of nh*stepm elementary matrices    Modification of warning when the covariates values are not 0 or
   and the contribution of each individual to the likelihood is simply    1.
   hPijx.    Version 0.98g
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.122  2006/03/20 09:45:41  brouard
   of the life expectancies. It also computes the prevalence limits.    (Module): Weights can have a decimal point as for
      English (a comma might work with a correct LC_NUMERIC environment,
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    otherwise the weight is truncated).
            Institut national d'études démographiques, Paris.    Modification of warning when the covariates values are not 0 or
   This software have been partly granted by Euro-REVES, a concerted action    1.
   from the European Union.    Version 0.98g
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.121  2006/03/16 17:45:01  lievre
   can be accessed at http://euroreves.ined.fr/imach .    * imach.c (Module): Comments concerning covariates added
   **********************************************************************/  
      * imach.c (Module): refinements in the computation of lli if
 #include <math.h>    status=-2 in order to have more reliable computation if stepm is
 #include <stdio.h>    not 1 month. Version 0.98f
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.120  2006/03/16 15:10:38  lievre
     (Module): refinements in the computation of lli if
 #define MAXLINE 256    status=-2 in order to have more reliable computation if stepm is
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    not 1 month. Version 0.98f
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.119  2006/03/15 17:42:26  brouard
 #define windows    (Module): Bug if status = -2, the loglikelihood was
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    computed as likelihood omitting the logarithm. Version O.98e
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.118  2006/03/14 18:20:07  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    (Module): varevsij Comments added explaining the second
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #define NINTERVMAX 8    (Module): Function pstamp added
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    (Module): Version 0.98d
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.117  2006/03/14 17:16:22  brouard
 #define MAXN 20000    (Module): varevsij Comments added explaining the second
 #define YEARM 12. /* Number of months per year */    table of variances if popbased=1 .
 #define AGESUP 130    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #define AGEBASE 40    (Module): Function pstamp added
     (Module): Version 0.98d
   
 int erreur; /* Error number */    Revision 1.116  2006/03/06 10:29:27  brouard
 int nvar;    (Module): Variance-covariance wrong links and
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    varian-covariance of ej. is needed (Saito).
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Revision 1.115  2006/02/27 12:17:45  brouard
 int ndeath=1; /* Number of dead states */    (Module): One freematrix added in mlikeli! 0.98c
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.114  2006/02/26 12:57:58  brouard
     (Module): Some improvements in processing parameter
 int *wav; /* Number of waves for this individuual 0 is possible */    filename with strsep.
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.113  2006/02/24 14:20:24  brouard
 int mle, weightopt;    (Module): Memory leaks checks with valgrind and:
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    datafile was not closed, some imatrix were not freed and on matrix
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    allocation too.
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.112  2006/01/30 09:55:26  brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;  
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    Revision 1.111  2006/01/25 20:38:18  brouard
 FILE *ficreseij;    (Module): Lots of cleaning and bugs added (Gompertz)
   char filerese[FILENAMELENGTH];    (Module): Comments can be added in data file. Missing date values
  FILE  *ficresvij;    can be a simple dot '.'.
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.110  2006/01/25 00:51:50  brouard
   char fileresvpl[FILENAMELENGTH];    (Module): Lots of cleaning and bugs added (Gompertz)
   
 #define NR_END 1    Revision 1.109  2006/01/24 19:37:15  brouard
 #define FREE_ARG char*    (Module): Comments (lines starting with a #) are allowed in data.
 #define FTOL 1.0e-10  
     Revision 1.108  2006/01/19 18:05:42  lievre
 #define NRANSI    Gnuplot problem appeared...
 #define ITMAX 200    To be fixed
   
 #define TOL 2.0e-4    Revision 1.107  2006/01/19 16:20:37  brouard
     Test existence of gnuplot in imach path
 #define CGOLD 0.3819660  
 #define ZEPS 1.0e-10    Revision 1.106  2006/01/19 13:24:36  brouard
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Some cleaning and links added in html output
   
 #define GOLD 1.618034    Revision 1.105  2006/01/05 20:23:19  lievre
 #define GLIMIT 100.0    *** empty log message ***
 #define TINY 1.0e-20  
     Revision 1.104  2005/09/30 16:11:43  lievre
 static double maxarg1,maxarg2;    (Module): sump fixed, loop imx fixed, and simplifications.
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    (Module): If the status is missing at the last wave but we know
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    that the person is alive, then we can code his/her status as -2
      (instead of missing=-1 in earlier versions) and his/her
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    contributions to the likelihood is 1 - Prob of dying from last
 #define rint(a) floor(a+0.5)    health status (= 1-p13= p11+p12 in the easiest case of somebody in
     the healthy state at last known wave). Version is 0.98
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.103  2005/09/30 15:54:49  lievre
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    (Module): sump fixed, loop imx fixed, and simplifications.
   
 int imx;    Revision 1.102  2004/09/15 17:31:30  brouard
 int stepm;    Add the possibility to read data file including tab characters.
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.101  2004/09/15 10:38:38  brouard
 int m,nb;    Fix on curr_time
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.100  2004/07/12 18:29:06  brouard
 double **pmmij, ***probs, ***mobaverage;    Add version for Mac OS X. Just define UNIX in Makefile
 double dateintmean=0;  
     Revision 1.99  2004/06/05 08:57:40  brouard
 double *weight;    *** empty log message ***
 int **s; /* Status */  
 double *agedc, **covar, idx;    Revision 1.98  2004/05/16 15:05:56  brouard
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    New version 0.97 . First attempt to estimate force of mortality
     directly from the data i.e. without the need of knowing the health
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    state at each age, but using a Gompertz model: log u =a + b*age .
 double ftolhess; /* Tolerance for computing hessian */    This is the basic analysis of mortality and should be done before any
     other analysis, in order to test if the mortality estimated from the
 /**************** split *************************/    cross-longitudinal survey is different from the mortality estimated
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    from other sources like vital statistic data.
 {  
    char *s;                             /* pointer */    The same imach parameter file can be used but the option for mle should be -3.
    int  l1, l2;                         /* length counters */  
     Agnès, who wrote this part of the code, tried to keep most of the
    l1 = strlen( path );                 /* length of path */    former routines in order to include the new code within the former code.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows    The output is very simple: only an estimate of the intercept and of
    s = strrchr( path, '\\' );           /* find last / */    the slope with 95% confident intervals.
 #else  
    s = strrchr( path, '/' );            /* find last / */    Current limitations:
 #endif    A) Even if you enter covariates, i.e. with the
    if ( s == NULL ) {                   /* no directory, so use current */    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #if     defined(__bsd__)                /* get current working directory */    B) There is no computation of Life Expectancy nor Life Table.
       extern char       *getwd( );  
     Revision 1.97  2004/02/20 13:25:42  lievre
       if ( getwd( dirc ) == NULL ) {    Version 0.96d. Population forecasting command line is (temporarily)
 #else    suppressed.
       extern char       *getcwd( );  
     Revision 1.96  2003/07/15 15:38:55  brouard
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #endif    rewritten within the same printf. Workaround: many printfs.
          return( GLOCK_ERROR_GETCWD );  
       }    Revision 1.95  2003/07/08 07:54:34  brouard
       strcpy( name, path );             /* we've got it */    * imach.c (Repository):
    } else {                             /* strip direcotry from path */    (Repository): Using imachwizard code to output a more meaningful covariance
       s++;                              /* after this, the filename */    matrix (cov(a12,c31) instead of numbers.
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.94  2003/06/27 13:00:02  brouard
       strcpy( name, s );                /* save file name */    Just cleaning
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.93  2003/06/25 16:33:55  brouard
    }    (Module): On windows (cygwin) function asctime_r doesn't
    l1 = strlen( dirc );                 /* length of directory */    exist so I changed back to asctime which exists.
 #ifdef windows    (Module): Version 0.96b
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else    Revision 1.92  2003/06/25 16:30:45  brouard
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    (Module): On windows (cygwin) function asctime_r doesn't
 #endif    exist so I changed back to asctime which exists.
    s = strrchr( name, '.' );            /* find last / */  
    s++;    Revision 1.91  2003/06/25 15:30:29  brouard
    strcpy(ext,s);                       /* save extension */    * imach.c (Repository): Duplicated warning errors corrected.
    l1= strlen( name);    (Repository): Elapsed time after each iteration is now output. It
    l2= strlen( s)+1;    helps to forecast when convergence will be reached. Elapsed time
    strncpy( finame, name, l1-l2);    is stamped in powell.  We created a new html file for the graphs
    finame[l1-l2]= 0;    concerning matrix of covariance. It has extension -cov.htm.
    return( 0 );                         /* we're done */  
 }    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 /******************************************/    of the covariance matrix to be input.
   
 void replace(char *s, char*t)    Revision 1.89  2003/06/24 12:30:52  brouard
 {    (Module): Some bugs corrected for windows. Also, when
   int i;    mle=-1 a template is output in file "or"mypar.txt with the design
   int lg=20;    of the covariance matrix to be input.
   i=0;  
   lg=strlen(t);    Revision 1.88  2003/06/23 17:54:56  brouard
   for(i=0; i<= lg; i++) {    * 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.
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Revision 1.87  2003/06/18 12:26:01  brouard
   }    Version 0.96
 }  
     Revision 1.86  2003/06/17 20:04:08  brouard
 int nbocc(char *s, char occ)    (Module): Change position of html and gnuplot routines and added
 {    routine fileappend.
   int i,j=0;  
   int lg=20;    Revision 1.85  2003/06/17 13:12:43  brouard
   i=0;    * imach.c (Repository): Check when date of death was earlier that
   lg=strlen(s);    current date of interview. It may happen when the death was just
   for(i=0; i<= lg; i++) {    prior to the death. In this case, dh was negative and likelihood
   if  (s[i] == occ ) j++;    was wrong (infinity). We still send an "Error" but patch by
   }    assuming that the date of death was just one stepm after the
   return j;    interview.
 }    (Repository): Because some people have very long ID (first column)
     we changed int to long in num[] and we added a new lvector for
 void cutv(char *u,char *v, char*t, char occ)    memory allocation. But we also truncated to 8 characters (left
 {    truncation)
   int i,lg,j,p=0;    (Repository): No more line truncation errors.
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    Revision 1.84  2003/06/13 21:44:43  brouard
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    * imach.c (Repository): Replace "freqsummary" at a correct
   }    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
   lg=strlen(t);    parcimony.
   for(j=0; j<p; j++) {    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
     (u[j] = t[j]);  
   }    Revision 1.83  2003/06/10 13:39:11  lievre
      u[p]='\0';    *** empty log message ***
   
    for(j=0; j<= lg; j++) {    Revision 1.82  2003/06/05 15:57:20  brouard
     if (j>=(p+1))(v[j-p-1] = t[j]);    Add log in  imach.c and  fullversion number is now printed.
   }  
 }  */
   /*
 /********************** nrerror ********************/     Interpolated Markov Chain
   
 void nrerror(char error_text[])    Short summary of the programme:
 {    
   fprintf(stderr,"ERREUR ...\n");    This program computes Healthy Life Expectancies from
   fprintf(stderr,"%s\n",error_text);    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   exit(1);    first survey ("cross") where individuals from different ages are
 }    interviewed on their health status or degree of disability (in the
 /*********************** vector *******************/    case of a health survey which is our main interest) -2- at least a
 double *vector(int nl, int nh)    second wave of interviews ("longitudinal") which measure each change
 {    (if any) in individual health status.  Health expectancies are
   double *v;    computed from the time spent in each health state according to a
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    model. More health states you consider, more time is necessary to reach the
   if (!v) nrerror("allocation failure in vector");    Maximum Likelihood of the parameters involved in the model.  The
   return v-nl+NR_END;    simplest model is the multinomial logistic model where pij is the
 }    probability to be observed in state j at the second wave
     conditional to be observed in state i at the first wave. Therefore
 /************************ free vector ******************/    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 void free_vector(double*v, int nl, int nh)    '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
   free((FREE_ARG)(v+nl-NR_END));    where the markup *Covariates have to be included here again* invites
 }    you to do it.  More covariates you add, slower the
     convergence.
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    The advantage of this computer programme, compared to a simple
 {    multinomial logistic model, is clear when the delay between waves is not
   int *v;    identical for each individual. Also, if a individual missed an
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    intermediate interview, the information is lost, but taken into
   if (!v) nrerror("allocation failure in ivector");    account using an interpolation or extrapolation.  
   return v-nl+NR_END;  
 }    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 ivector **************************/    split into an exact number (nh*stepm) of unobserved intermediate
 void free_ivector(int *v, long nl, long nh)    states. This elementary transition (by month, quarter,
 {    semester or year) is modelled as a multinomial logistic.  The hPx
   free((FREE_ARG)(v+nl-NR_END));    matrix is simply the matrix product of nh*stepm elementary matrices
 }    and the contribution of each individual to the likelihood is simply
     hPijx.
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)    Also this programme outputs the covariance matrix of the parameters but also
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    of the life expectancies. It also computes the period (stable) prevalence. 
 {    
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   int **m;             Institut national d'études démographiques, Paris.
      This software have been partly granted by Euro-REVES, a concerted action
   /* allocate pointers to rows */    from the European Union.
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    It is copyrighted identically to a GNU software product, ie programme and
   if (!m) nrerror("allocation failure 1 in matrix()");    software can be distributed freely for non commercial use. Latest version
   m += NR_END;    can be accessed at http://euroreves.ined.fr/imach .
   m -= nrl;  
      Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
      or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   /* allocate rows and set pointers to them */    
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    **********************************************************************/
   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
      freqsummary
   /* return pointer to array of pointers to rows */    if (mle >= 1)
   return m;      mlikeli
 }    print results files
     if mle==1 
 /****************** free_imatrix *************************/       computes hessian
 void free_imatrix(m,nrl,nrh,ncl,nch)    read end of parameter file: agemin, agemax, bage, fage, estepm
       int **m;        begin-prev-date,...
       long nch,ncl,nrh,nrl;    open gnuplot file
      /* free an int matrix allocated by imatrix() */    open html file
 {    period (stable) prevalence
   free((FREE_ARG) (m[nrl]+ncl-NR_END));     for age prevalim()
   free((FREE_ARG) (m+nrl-NR_END));    h Pij x
 }    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
 /******************* matrix *******************************/    health expectancies
 double **matrix(long nrl, long nrh, long ncl, long nch)    Variance-covariance of DFLE
 {    prevalence()
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;     movingaverage()
   double **m;    varevsij() 
     if popbased==1 varevsij(,popbased)
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    total life expectancies
   if (!m) nrerror("allocation failure 1 in matrix()");    Variance of period (stable) prevalence
   m += NR_END;   end
   m -= nrl;  */
   
   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;  #include <math.h>
   #include <stdio.h>
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #include <stdlib.h>
   return m;  #include <string.h>
 }  #include <unistd.h>
   
 /*************************free matrix ************************/  #include <limits.h>
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  #include <sys/types.h>
 {  #include <sys/stat.h>
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #include <errno.h>
   free((FREE_ARG)(m+nrl-NR_END));  extern int errno;
 }  
   /* #include <sys/time.h> */
 /******************* ma3x *******************************/  #include <time.h>
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  #include "timeval.h"
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  /* #include <libintl.h> */
   double ***m;  /* #define _(String) gettext (String) */
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define MAXLINE 256
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  #define GNUPLOTPROGRAM "gnuplot"
   m -= nrl;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   m[nrl] += NR_END;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   m[nrl] -= ncl;  
   #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #define NINTERVMAX 8
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   m[nrl][ncl] += NR_END;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   m[nrl][ncl] -= nll;  #define NCOVMAX 8 /* Maximum number of covariates */
   for (j=ncl+1; j<=nch; j++)  #define MAXN 20000
     m[nrl][j]=m[nrl][j-1]+nlay;  #define YEARM 12. /* Number of months per year */
    #define AGESUP 130
   for (i=nrl+1; i<=nrh; i++) {  #define AGEBASE 40
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
     for (j=ncl+1; j<=nch; j++)  #ifdef UNIX
       m[i][j]=m[i][j-1]+nlay;  #define DIRSEPARATOR '/'
   }  #define CHARSEPARATOR "/"
   return m;  #define ODIRSEPARATOR '\\'
 }  #else
   #define DIRSEPARATOR '\\'
 /*************************free ma3x ************************/  #define CHARSEPARATOR "\\"
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define ODIRSEPARATOR '/'
 {  #endif
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  /* $Id$ */
   free((FREE_ARG)(m+nrl-NR_END));  /* $State$ */
 }  
   char version[]="Imach version 0.98h, April 2006, INED-EUROREVES-Institut de longevite ";
 /***************** f1dim *************************/  char fullversion[]="$Revision$ $Date$"; 
 extern int ncom;  char strstart[80];
 extern double *pcom,*xicom;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 extern double (*nrfunc)(double []);  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
    int nvar;
 double f1dim(double x)  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 {  int npar=NPARMAX;
   int j;  int nlstate=2; /* Number of live states */
   double f;  int ndeath=1; /* Number of dead states */
   double *xt;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
    int popbased=0;
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  int *wav; /* Number of waves for this individuual 0 is possible */
   f=(*nrfunc)(xt);  int maxwav; /* Maxim number of waves */
   free_vector(xt,1,ncom);  int jmin, jmax; /* min, max spacing between 2 waves */
   return f;  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
 }  int gipmx, gsw; /* Global variables on the number of contributions 
                      to the likelihood and the sum of weights (done by funcone)*/
 /*****************brent *************************/  int mle, weightopt;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 {  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int iter;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   double a,b,d,etemp;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double fu,fv,fw,fx;  double jmean; /* Mean space between 2 waves */
   double ftemp;  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   double e=0.0;  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
    FILE *ficlog, *ficrespow;
   a=(ax < cx ? ax : cx);  int globpr; /* Global variable for printing or not */
   b=(ax > cx ? ax : cx);  double fretone; /* Only one call to likelihood */
   x=w=v=bx;  long ipmx; /* Number of contributions */
   fw=fv=fx=(*f)(x);  double sw; /* Sum of weights */
   for (iter=1;iter<=ITMAX;iter++) {  char filerespow[FILENAMELENGTH];
     xm=0.5*(a+b);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  FILE *ficresilk;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     printf(".");fflush(stdout);  FILE *ficresprobmorprev;
 #ifdef DEBUG  FILE *fichtm, *fichtmcov; /* Html File */
     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);  FILE *ficreseij;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  char filerese[FILENAMELENGTH];
 #endif  FILE *ficresstdeij;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  char fileresstde[FILENAMELENGTH];
       *xmin=x;  FILE *ficrescveij;
       return fx;  char filerescve[FILENAMELENGTH];
     }  FILE  *ficresvij;
     ftemp=fu;  char fileresv[FILENAMELENGTH];
     if (fabs(e) > tol1) {  FILE  *ficresvpl;
       r=(x-w)*(fx-fv);  char fileresvpl[FILENAMELENGTH];
       q=(x-v)*(fx-fw);  char title[MAXLINE];
       p=(x-v)*q-(x-w)*r;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       q=2.0*(q-r);  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       if (q > 0.0) p = -p;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       q=fabs(q);  char command[FILENAMELENGTH];
       etemp=e;  int  outcmd=0;
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {  char filelog[FILENAMELENGTH]; /* Log file */
         d=p/q;  char filerest[FILENAMELENGTH];
         u=x+d;  char fileregp[FILENAMELENGTH];
         if (u-a < tol2 || b-u < tol2)  char popfile[FILENAMELENGTH];
           d=SIGN(tol1,xm-x);  
       }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
     }  struct timezone tzp;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  extern int gettimeofday();
     fu=(*f)(u);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
     if (fu <= fx) {  long time_value;
       if (u >= x) a=x; else b=x;  extern long time();
       SHFT(v,w,x,u)  char strcurr[80], strfor[80];
         SHFT(fv,fw,fx,fu)  
         } else {  char *endptr;
           if (u < x) a=u; else b=u;  long lval;
           if (fu <= fw || w == x) {  double dval;
             v=w;  
             w=u;  #define NR_END 1
             fv=fw;  #define FREE_ARG char*
             fw=fu;  #define FTOL 1.0e-10
           } else if (fu <= fv || v == x || v == w) {  
             v=u;  #define NRANSI 
             fv=fu;  #define ITMAX 200 
           }  
         }  #define TOL 2.0e-4 
   }  
   nrerror("Too many iterations in brent");  #define CGOLD 0.3819660 
   *xmin=x;  #define ZEPS 1.0e-10 
   return fx;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 }  
   #define GOLD 1.618034 
 /****************** mnbrak ***********************/  #define GLIMIT 100.0 
   #define TINY 1.0e-20 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))  static double maxarg1,maxarg2;
 {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   double ulim,u,r,q, dum;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   double fu;    
    #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   *fa=(*func)(*ax);  #define rint(a) floor(a+0.5)
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  static double sqrarg;
     SHFT(dum,*ax,*bx,dum)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       SHFT(dum,*fb,*fa,dum)  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       }  int agegomp= AGEGOMP;
   *cx=(*bx)+GOLD*(*bx-*ax);  
   *fc=(*func)(*cx);  int imx; 
   while (*fb > *fc) {  int stepm=1;
     r=(*bx-*ax)*(*fb-*fc);  /* Stepm, step in month: minimum step interpolation*/
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  int estepm;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {  int m,nb;
       fu=(*func)(u);  long *num;
     } else if ((*cx-u)*(u-ulim) > 0.0) {  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       fu=(*func)(u);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       if (fu < *fc) {  double **pmmij, ***probs;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  double *ageexmed,*agecens;
           SHFT(*fb,*fc,fu,(*func)(u))  double dateintmean=0;
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  double *weight;
       u=ulim;  int **s; /* Status */
       fu=(*func)(u);  double *agedc, **covar, idx;
     } else {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       u=(*cx)+GOLD*(*cx-*bx);  double *lsurv, *lpop, *tpop;
       fu=(*func)(u);  
     }  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
     SHFT(*ax,*bx,*cx,u)  double ftolhess; /* Tolerance for computing hessian */
       SHFT(*fa,*fb,*fc,fu)  
       }  /**************** split *************************/
 }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
 /*************** linmin ************************/    /* 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)
 int ncom;    */ 
 double *pcom,*xicom;    char  *ss;                            /* pointer */
 double (*nrfunc)(double []);    int   l1, l2;                         /* length counters */
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    l1 = strlen(path );                   /* length of path */
 {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   double brent(double ax, double bx, double cx,    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
                double (*f)(double), double tol, double *xmin);    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   double f1dim(double x);      strcpy( name, path );               /* we got the fullname name because no directory */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
               double *fc, double (*func)(double));        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   int j;      /* get current working directory */
   double xx,xmin,bx,ax;      /*    extern  char* getcwd ( char *buf , int len);*/
   double fx,fb,fa;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
          return( GLOCK_ERROR_GETCWD );
   ncom=n;      }
   pcom=vector(1,n);      /* got dirc from getcwd*/
   xicom=vector(1,n);      printf(" DIRC = %s \n",dirc);
   nrfunc=func;    } else {                              /* strip direcotry from path */
   for (j=1;j<=n;j++) {      ss++;                               /* after this, the filename */
     pcom[j]=p[j];      l2 = strlen( ss );                  /* length of filename */
     xicom[j]=xi[j];      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   }      strcpy( name, ss );         /* save file name */
   ax=0.0;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   xx=1.0;      dirc[l1-l2] = 0;                    /* add zero */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      printf(" DIRC2 = %s \n",dirc);
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    }
 #ifdef DEBUG    /* We add a separator at the end of dirc if not exists */
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    l1 = strlen( dirc );                  /* length of directory */
 #endif    if( dirc[l1-1] != DIRSEPARATOR ){
   for (j=1;j<=n;j++) {      dirc[l1] =  DIRSEPARATOR;
     xi[j] *= xmin;      dirc[l1+1] = 0; 
     p[j] += xi[j];      printf(" DIRC3 = %s \n",dirc);
   }    }
   free_vector(xicom,1,n);    ss = strrchr( name, '.' );            /* find last / */
   free_vector(pcom,1,n);    if (ss >0){
 }      ss++;
       strcpy(ext,ss);                     /* save extension */
 /*************** powell ************************/      l1= strlen( name);
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      l2= strlen(ss)+1;
             double (*func)(double []))      strncpy( finame, name, l1-l2);
 {      finame[l1-l2]= 0;
   void linmin(double p[], double xi[], int n, double *fret,    }
               double (*func)(double []));  
   int i,ibig,j;    return( 0 );                          /* we're done */
   double del,t,*pt,*ptt,*xit;  }
   double fp,fptt;  
   double *xits;  
   pt=vector(1,n);  /******************************************/
   ptt=vector(1,n);  
   xit=vector(1,n);  void replace_back_to_slash(char *s, char*t)
   xits=vector(1,n);  {
   *fret=(*func)(p);    int i;
   for (j=1;j<=n;j++) pt[j]=p[j];    int lg=0;
   for (*iter=1;;++(*iter)) {    i=0;
     fp=(*fret);    lg=strlen(t);
     ibig=0;    for(i=0; i<= lg; i++) {
     del=0.0;      (s[i] = t[i]);
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      if (t[i]== '\\') s[i]='/';
     for (i=1;i<=n;i++)    }
       printf(" %d %.12f",i, p[i]);  }
     printf("\n");  
     for (i=1;i<=n;i++) {  int nbocc(char *s, char occ)
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  {
       fptt=(*fret);    int i,j=0;
 #ifdef DEBUG    int lg=20;
       printf("fret=%lf \n",*fret);    i=0;
 #endif    lg=strlen(s);
       printf("%d",i);fflush(stdout);    for(i=0; i<= lg; i++) {
       linmin(p,xit,n,fret,func);    if  (s[i] == occ ) j++;
       if (fabs(fptt-(*fret)) > del) {    }
         del=fabs(fptt-(*fret));    return j;
         ibig=i;  }
       }  
 #ifdef DEBUG  void cutv(char *u,char *v, char*t, char occ)
       printf("%d %.12e",i,(*fret));  {
       for (j=1;j<=n;j++) {    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
         printf(" x(%d)=%.12e",j,xit[j]);       gives u="abcedf" and v="ghi2j" */
       }    int i,lg,j,p=0;
       for(j=1;j<=n;j++)    i=0;
         printf(" p=%.12e",p[j]);    for(j=0; j<=strlen(t)-1; j++) {
       printf("\n");      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 #endif    }
     }  
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    lg=strlen(t);
 #ifdef DEBUG    for(j=0; j<p; j++) {
       int k[2],l;      (u[j] = t[j]);
       k[0]=1;    }
       k[1]=-1;       u[p]='\0';
       printf("Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++)     for(j=0; j<= lg; j++) {
         printf(" %.12e",p[j]);      if (j>=(p+1))(v[j-p-1] = t[j]);
       printf("\n");    }
       for(l=0;l<=1;l++) {  }
         for (j=1;j<=n;j++) {  
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  /********************** nrerror ********************/
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
         }  void nrerror(char error_text[])
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  {
       }    fprintf(stderr,"ERREUR ...\n");
 #endif    fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
   }
       free_vector(xit,1,n);  /*********************** vector *******************/
       free_vector(xits,1,n);  double *vector(int nl, int nh)
       free_vector(ptt,1,n);  {
       free_vector(pt,1,n);    double *v;
       return;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     }    if (!v) nrerror("allocation failure in vector");
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    return v-nl+NR_END;
     for (j=1;j<=n;j++) {  }
       ptt[j]=2.0*p[j]-pt[j];  
       xit[j]=p[j]-pt[j];  /************************ free vector ******************/
       pt[j]=p[j];  void free_vector(double*v, int nl, int nh)
     }  {
     fptt=(*func)(ptt);    free((FREE_ARG)(v+nl-NR_END));
     if (fptt < fp) {  }
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {  /************************ivector *******************************/
         linmin(p,xit,n,fret,func);  int *ivector(long nl,long nh)
         for (j=1;j<=n;j++) {  {
           xi[j][ibig]=xi[j][n];    int *v;
           xi[j][n]=xit[j];    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
         }    if (!v) nrerror("allocation failure in ivector");
 #ifdef DEBUG    return v-nl+NR_END;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  }
         for(j=1;j<=n;j++)  
           printf(" %.12e",xit[j]);  /******************free ivector **************************/
         printf("\n");  void free_ivector(int *v, long nl, long nh)
 #endif  {
       }    free((FREE_ARG)(v+nl-NR_END));
     }  }
   }  
 }  /************************lvector *******************************/
   long *lvector(long nl,long nh)
 /**** Prevalence limit ****************/  {
     long *v;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 {    if (!v) nrerror("allocation failure in ivector");
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    return v-nl+NR_END;
      matrix by transitions matrix until convergence is reached */  }
   
   int i, ii,j,k;  /******************free lvector **************************/
   double min, max, maxmin, maxmax,sumnew=0.;  void free_lvector(long *v, long nl, long nh)
   double **matprod2();  {
   double **out, cov[NCOVMAX], **pmij();    free((FREE_ARG)(v+nl-NR_END));
   double **newm;  }
   double agefin, delaymax=50 ; /* Max number of years to converge */  
   /******************* imatrix *******************************/
   for (ii=1;ii<=nlstate+ndeath;ii++)  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     for (j=1;j<=nlstate+ndeath;j++){       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  { 
     }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     int **m; 
    cov[1]=1.;    
      /* allocate pointers to rows */ 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    if (!m) nrerror("allocation failure 1 in matrix()"); 
     newm=savm;    m += NR_END; 
     /* Covariates have to be included here again */    m -= nrl; 
      cov[2]=agefin;    
      
       for (k=1; k<=cptcovn;k++) {    /* allocate rows and set pointers to them */ 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       }    m[nrl] += NR_END; 
       for (k=1; k<=cptcovage;k++)    m[nrl] -= ncl; 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    
       for (k=1; k<=cptcovprod;k++)    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    
     /* return pointer to array of pointers to rows */ 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    return m; 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  } 
   
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
     savm=oldm;        int **m;
     oldm=newm;        long nch,ncl,nrh,nrl; 
     maxmax=0.;       /* free an int matrix allocated by imatrix() */ 
     for(j=1;j<=nlstate;j++){  { 
       min=1.;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       max=0.;    free((FREE_ARG) (m+nrl-NR_END)); 
       for(i=1; i<=nlstate; i++) {  } 
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  /******************* matrix *******************************/
         prlim[i][j]= newm[i][j]/(1-sumnew);  double **matrix(long nrl, long nrh, long ncl, long nch)
         max=FMAX(max,prlim[i][j]);  {
         min=FMIN(min,prlim[i][j]);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       }    double **m;
       maxmin=max-min;  
       maxmax=FMAX(maxmax,maxmin);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     }    if (!m) nrerror("allocation failure 1 in matrix()");
     if(maxmax < ftolpl){    m += NR_END;
       return prlim;    m -= nrl;
     }  
   }    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;
 /*************** transition probabilities ***************/    m[nrl] -= ncl;
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 {    return m;
   double s1, s2;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
   /*double t34;*/     */
   int i,j,j1, nc, ii, jj;  }
   
     for(i=1; i<= nlstate; i++){  /*************************free matrix ************************/
     for(j=1; j<i;j++){  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  {
         /*s2 += param[i][j][nc]*cov[nc];*/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    free((FREE_ARG)(m+nrl-NR_END));
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  }
       }  
       ps[i][j]=s2;  /******************* ma3x *******************************/
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     }  {
     for(j=i+1; j<=nlstate+ndeath;j++){    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    double ***m;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       }    if (!m) nrerror("allocation failure 1 in matrix()");
       ps[i][j]=s2;    m += NR_END;
     }    m -= nrl;
   }  
     /*ps[3][2]=1;*/    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   for(i=1; i<= nlstate; i++){    m[nrl] += NR_END;
      s1=0;    m[nrl] -= ncl;
     for(j=1; j<i; j++)  
       s1+=exp(ps[i][j]);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     for(j=i+1; j<=nlstate+ndeath; j++)  
       s1+=exp(ps[i][j]);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     ps[i][i]=1./(s1+1.);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     for(j=1; j<i; j++)    m[nrl][ncl] += NR_END;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    m[nrl][ncl] -= nll;
     for(j=i+1; j<=nlstate+ndeath; j++)    for (j=ncl+1; j<=nch; j++) 
       ps[i][j]= exp(ps[i][j])*ps[i][i];      m[nrl][j]=m[nrl][j-1]+nlay;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    
   } /* end i */    for (i=nrl+1; i<=nrh; i++) {
       m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      for (j=ncl+1; j<=nch; j++) 
     for(jj=1; jj<= nlstate+ndeath; jj++){        m[i][j]=m[i][j-1]+nlay;
       ps[ii][jj]=0;    }
       ps[ii][ii]=1;    return m; 
     }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   }             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     */
   }
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  /*************************free ma3x ************************/
      printf("%lf ",ps[ii][jj]);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
    }  {
     printf("\n ");    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     printf("\n ");printf("%lf ",cov[2]);*/    free((FREE_ARG)(m+nrl-NR_END));
 /*  }
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  
   goto end;*/  /*************** function subdirf ***********/
     return ps;  char *subdirf(char fileres[])
 }  {
     /* Caution optionfilefiname is hidden */
 /**************** Product of 2 matrices ******************/    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    strcat(tmpout,fileres);
 {    return tmpout;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  }
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized  /*************** function subdirf2 ***********/
      before: only the contents of out is modified. The function returns  char *subdirf2(char fileres[], char *preop)
      a pointer to pointers identical to out */  {
   long i, j, k;    
   for(i=nrl; i<= nrh; i++)    /* Caution optionfilefiname is hidden */
     for(k=ncolol; k<=ncoloh; k++)    strcpy(tmpout,optionfilefiname);
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    strcat(tmpout,"/");
         out[i][k] +=in[i][j]*b[j][k];    strcat(tmpout,preop);
     strcat(tmpout,fileres);
   return out;    return tmpout;
 }  }
   
   /*************** function subdirf3 ***********/
 /************* Higher Matrix Product ***************/  char *subdirf3(char fileres[], char *preop, char *preop2)
   {
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    
 {    /* Caution optionfilefiname is hidden */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    strcpy(tmpout,optionfilefiname);
      duration (i.e. until    strcat(tmpout,"/");
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    strcat(tmpout,preop);
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    strcat(tmpout,preop2);
      (typically every 2 years instead of every month which is too big).    strcat(tmpout,fileres);
      Model is determined by parameters x and covariates have to be    return tmpout;
      included manually here.  }
   
      */  /***************** f1dim *************************/
   extern int ncom; 
   int i, j, d, h, k;  extern double *pcom,*xicom;
   double **out, cov[NCOVMAX];  extern double (*nrfunc)(double []); 
   double **newm;   
   double f1dim(double x) 
   /* Hstepm could be zero and should return the unit matrix */  { 
   for (i=1;i<=nlstate+ndeath;i++)    int j; 
     for (j=1;j<=nlstate+ndeath;j++){    double f;
       oldm[i][j]=(i==j ? 1.0 : 0.0);    double *xt; 
       po[i][j][0]=(i==j ? 1.0 : 0.0);   
     }    xt=vector(1,ncom); 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   for(h=1; h <=nhstepm; h++){    f=(*nrfunc)(xt); 
     for(d=1; d <=hstepm; d++){    free_vector(xt,1,ncom); 
       newm=savm;    return f; 
       /* Covariates have to be included here again */  } 
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  /*****************brent *************************/
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       for (k=1; k<=cptcovage;k++)  { 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    int iter; 
       for (k=1; k<=cptcovprod;k++)    double a,b,d,etemp;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    double fu,fv,fw,fx;
     double ftemp;
     double p,q,r,tol1,tol2,u,v,w,x,xm; 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    double e=0.0; 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/   
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    a=(ax < cx ? ax : cx); 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    b=(ax > cx ? ax : cx); 
       savm=oldm;    x=w=v=bx; 
       oldm=newm;    fw=fv=fx=(*f)(x); 
     }    for (iter=1;iter<=ITMAX;iter++) { 
     for(i=1; i<=nlstate+ndeath; i++)      xm=0.5*(a+b); 
       for(j=1;j<=nlstate+ndeath;j++) {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         po[i][j][h]=newm[i][j];      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      printf(".");fflush(stdout);
          */      fprintf(ficlog,".");fflush(ficlog);
       }  #ifdef DEBUG
   } /* end h */      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);
   return po;      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   #endif
       if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 /*************** log-likelihood *************/        *xmin=x; 
 double func( double *x)        return fx; 
 {      } 
   int i, ii, j, k, mi, d, kk;      ftemp=fu;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      if (fabs(e) > tol1) { 
   double **out;        r=(x-w)*(fx-fv); 
   double sw; /* Sum of weights */        q=(x-v)*(fx-fw); 
   double lli; /* Individual log likelihood */        p=(x-v)*q-(x-w)*r; 
   long ipmx;        q=2.0*(q-r); 
   /*extern weight */        if (q > 0.0) p = -p; 
   /* We are differentiating ll according to initial status */        q=fabs(q); 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        etemp=e; 
   /*for(i=1;i<imx;i++)        e=d; 
     printf(" %d\n",s[4][i]);        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)); 
   cov[1]=1.;        else { 
           d=p/q; 
   for(k=1; k<=nlstate; k++) ll[k]=0.;          u=x+d; 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){          if (u-a < tol2 || b-u < tol2) 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];            d=SIGN(tol1,xm-x); 
     for(mi=1; mi<= wav[i]-1; mi++){        } 
       for (ii=1;ii<=nlstate+ndeath;ii++)      } else { 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for(d=0; d<dh[mi][i]; d++){      } 
         newm=savm;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      fu=(*f)(u); 
         for (kk=1; kk<=cptcovage;kk++) {      if (fu <= fx) { 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        if (u >= x) a=x; else b=x; 
         }        SHFT(v,w,x,u) 
                  SHFT(fv,fw,fx,fu) 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          } else { 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));            if (u < x) a=u; else b=u; 
         savm=oldm;            if (fu <= fw || w == x) { 
         oldm=newm;              v=w; 
                      w=u; 
                      fv=fw; 
       } /* end mult */              fw=fu; 
                  } else if (fu <= fv || v == x || v == w) { 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);              v=u; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/              fv=fu; 
       ipmx +=1;            } 
       sw += weight[i];          } 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    } 
     } /* end of wave */    nrerror("Too many iterations in brent"); 
   } /* end of individual */    *xmin=x; 
     return fx; 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  } 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  /****************** mnbrak ***********************/
   return -l;  
 }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               double (*func)(double)) 
   { 
 /*********** Maximum Likelihood Estimation ***************/    double ulim,u,r,q, dum;
     double fu; 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))   
 {    *fa=(*func)(*ax); 
   int i,j, iter;    *fb=(*func)(*bx); 
   double **xi,*delti;    if (*fb > *fa) { 
   double fret;      SHFT(dum,*ax,*bx,dum) 
   xi=matrix(1,npar,1,npar);        SHFT(dum,*fb,*fa,dum) 
   for (i=1;i<=npar;i++)        } 
     for (j=1;j<=npar;j++)    *cx=(*bx)+GOLD*(*bx-*ax); 
       xi[i][j]=(i==j ? 1.0 : 0.0);    *fc=(*func)(*cx); 
   printf("Powell\n");    while (*fb > *fc) { 
   powell(p,xi,npar,ftol,&iter,&fret,func);      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
 }      if ((*bx-u)*(u-*cx) > 0.0) { 
         fu=(*func)(u); 
 /**** Computes Hessian and covariance matrix ***/      } else if ((*cx-u)*(u-ulim) > 0.0) { 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        fu=(*func)(u); 
 {        if (fu < *fc) { 
   double  **a,**y,*x,pd;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double **hess;            SHFT(*fb,*fc,fu,(*func)(u)) 
   int i, j,jk;            } 
   int *indx;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         u=ulim; 
   double hessii(double p[], double delta, int theta, double delti[]);        fu=(*func)(u); 
   double hessij(double p[], double delti[], int i, int j);      } else { 
   void lubksb(double **a, int npar, int *indx, double b[]) ;        u=(*cx)+GOLD*(*cx-*bx); 
   void ludcmp(double **a, int npar, int *indx, double *d) ;        fu=(*func)(u); 
       } 
   hess=matrix(1,npar,1,npar);      SHFT(*ax,*bx,*cx,u) 
         SHFT(*fa,*fb,*fc,fu) 
   printf("\nCalculation of the hessian matrix. Wait...\n");        } 
   for (i=1;i<=npar;i++){  } 
     printf("%d",i);fflush(stdout);  
     hess[i][i]=hessii(p,ftolhess,i,delti);  /*************** linmin ************************/
     /*printf(" %f ",p[i]);*/  
     /*printf(" %lf ",hess[i][i]);*/  int ncom; 
   }  double *pcom,*xicom;
    double (*nrfunc)(double []); 
   for (i=1;i<=npar;i++) {   
     for (j=1;j<=npar;j++)  {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       if (j>i) {  { 
         printf(".%d%d",i,j);fflush(stdout);    double brent(double ax, double bx, double cx, 
         hess[i][j]=hessij(p,delti,i,j);                 double (*f)(double), double tol, double *xmin); 
         hess[j][i]=hess[i][j];        double f1dim(double x); 
         /*printf(" %lf ",hess[i][j]);*/    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       }                double *fc, double (*func)(double)); 
     }    int j; 
   }    double xx,xmin,bx,ax; 
   printf("\n");    double fx,fb,fa;
    
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    ncom=n; 
      pcom=vector(1,n); 
   a=matrix(1,npar,1,npar);    xicom=vector(1,n); 
   y=matrix(1,npar,1,npar);    nrfunc=func; 
   x=vector(1,npar);    for (j=1;j<=n;j++) { 
   indx=ivector(1,npar);      pcom[j]=p[j]; 
   for (i=1;i<=npar;i++)      xicom[j]=xi[j]; 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    } 
   ludcmp(a,npar,indx,&pd);    ax=0.0; 
     xx=1.0; 
   for (j=1;j<=npar;j++) {    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     for (i=1;i<=npar;i++) x[i]=0;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     x[j]=1;  #ifdef DEBUG
     lubksb(a,npar,indx,x);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     for (i=1;i<=npar;i++){    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       matcov[i][j]=x[i];  #endif
     }    for (j=1;j<=n;j++) { 
   }      xi[j] *= xmin; 
       p[j] += xi[j]; 
   printf("\n#Hessian matrix#\n");    } 
   for (i=1;i<=npar;i++) {    free_vector(xicom,1,n); 
     for (j=1;j<=npar;j++) {    free_vector(pcom,1,n); 
       printf("%.3e ",hess[i][j]);  } 
     }  
     printf("\n");  char *asc_diff_time(long time_sec, char ascdiff[])
   }  {
     long sec_left, days, hours, minutes;
   /* Recompute Inverse */    days = (time_sec) / (60*60*24);
   for (i=1;i<=npar;i++)    sec_left = (time_sec) % (60*60*24);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    hours = (sec_left) / (60*60) ;
   ludcmp(a,npar,indx,&pd);    sec_left = (sec_left) %(60*60);
     minutes = (sec_left) /60;
   /*  printf("\n#Hessian matrix recomputed#\n");    sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   for (j=1;j<=npar;j++) {    return ascdiff;
     for (i=1;i<=npar;i++) x[i]=0;  }
     x[j]=1;  
     lubksb(a,npar,indx,x);  /*************** powell ************************/
     for (i=1;i<=npar;i++){  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       y[i][j]=x[i];              double (*func)(double [])) 
       printf("%.3e ",y[i][j]);  { 
     }    void linmin(double p[], double xi[], int n, double *fret, 
     printf("\n");                double (*func)(double [])); 
   }    int i,ibig,j; 
   */    double del,t,*pt,*ptt,*xit;
     double fp,fptt;
   free_matrix(a,1,npar,1,npar);    double *xits;
   free_matrix(y,1,npar,1,npar);    int niterf, itmp;
   free_vector(x,1,npar);  
   free_ivector(indx,1,npar);    pt=vector(1,n); 
   free_matrix(hess,1,npar,1,npar);    ptt=vector(1,n); 
     xit=vector(1,n); 
     xits=vector(1,n); 
 }    *fret=(*func)(p); 
     for (j=1;j<=n;j++) pt[j]=p[j]; 
 /*************** hessian matrix ****************/    for (*iter=1;;++(*iter)) { 
 double hessii( double x[], double delta, int theta, double delti[])      fp=(*fret); 
 {      ibig=0; 
   int i;      del=0.0; 
   int l=1, lmax=20;      last_time=curr_time;
   double k1,k2;      (void) gettimeofday(&curr_time,&tzp);
   double p2[NPARMAX+1];      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);
   double res;      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);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
   double fx;     for (i=1;i<=n;i++) {
   int k=0,kmax=10;        printf(" %d %.12f",i, p[i]);
   double l1;        fprintf(ficlog," %d %.12lf",i, p[i]);
         fprintf(ficrespow," %.12lf", p[i]);
   fx=func(x);      }
   for (i=1;i<=npar;i++) p2[i]=x[i];      printf("\n");
   for(l=0 ; l <=lmax; l++){      fprintf(ficlog,"\n");
     l1=pow(10,l);      fprintf(ficrespow,"\n");fflush(ficrespow);
     delts=delt;      if(*iter <=3){
     for(k=1 ; k <kmax; k=k+1){        tm = *localtime(&curr_time.tv_sec);
       delt = delta*(l1*k);        strcpy(strcurr,asctime(&tm));
       p2[theta]=x[theta] +delt;  /*       asctime_r(&tm,strcurr); */
       k1=func(p2)-fx;        forecast_time=curr_time; 
       p2[theta]=x[theta]-delt;        itmp = strlen(strcurr);
       k2=func(p2)-fx;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
       /*res= (k1-2.0*fx+k2)/delt/delt; */          strcurr[itmp-1]='\0';
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
              fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
 #ifdef DEBUG        for(niterf=10;niterf<=30;niterf+=10){
       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);          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
 #endif          tmf = *localtime(&forecast_time.tv_sec);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  /*      asctime_r(&tmf,strfor); */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          strcpy(strfor,asctime(&tmf));
         k=kmax;          itmp = strlen(strfor);
       }          if(strfor[itmp-1]=='\n')
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          strfor[itmp-1]='\0';
         k=kmax; l=lmax*10.;          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       }          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        }
         delts=delt;      }
       }      for (i=1;i<=n;i++) { 
     }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   }        fptt=(*fret); 
   delti[theta]=delts;  #ifdef DEBUG
   return res;        printf("fret=%lf \n",*fret);
          fprintf(ficlog,"fret=%lf \n",*fret);
 }  #endif
         printf("%d",i);fflush(stdout);
 double hessij( double x[], double delti[], int thetai,int thetaj)        fprintf(ficlog,"%d",i);fflush(ficlog);
 {        linmin(p,xit,n,fret,func); 
   int i;        if (fabs(fptt-(*fret)) > del) { 
   int l=1, l1, lmax=20;          del=fabs(fptt-(*fret)); 
   double k1,k2,k3,k4,res,fx;          ibig=i; 
   double p2[NPARMAX+1];        } 
   int k;  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
   fx=func(x);        fprintf(ficlog,"%d %.12e",i,(*fret));
   for (k=1; k<=2; k++) {        for (j=1;j<=n;j++) {
     for (i=1;i<=npar;i++) p2[i]=x[i];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     p2[thetai]=x[thetai]+delti[thetai]/k;          printf(" x(%d)=%.12e",j,xit[j]);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     k1=func(p2)-fx;        }
          for(j=1;j<=n;j++) {
     p2[thetai]=x[thetai]+delti[thetai]/k;          printf(" p=%.12e",p[j]);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          fprintf(ficlog," p=%.12e",p[j]);
     k2=func(p2)-fx;        }
          printf("\n");
     p2[thetai]=x[thetai]-delti[thetai]/k;        fprintf(ficlog,"\n");
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  #endif
     k3=func(p2)-fx;      } 
        if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     p2[thetai]=x[thetai]-delti[thetai]/k;  #ifdef DEBUG
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        int k[2],l;
     k4=func(p2)-fx;        k[0]=1;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        k[1]=-1;
 #ifdef DEBUG        printf("Max: %.12e",(*func)(p));
     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,"Max: %.12e",(*func)(p));
 #endif        for (j=1;j<=n;j++) {
   }          printf(" %.12e",p[j]);
   return res;          fprintf(ficlog," %.12e",p[j]);
 }        }
         printf("\n");
 /************** Inverse of matrix **************/        fprintf(ficlog,"\n");
 void ludcmp(double **a, int n, int *indx, double *d)        for(l=0;l<=1;l++) {
 {          for (j=1;j<=n;j++) {
   int i,imax,j,k;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   double big,dum,sum,temp;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   double *vv;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
            }
   vv=vector(1,n);          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   *d=1.0;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   for (i=1;i<=n;i++) {        }
     big=0.0;  #endif
     for (j=1;j<=n;j++)  
       if ((temp=fabs(a[i][j])) > big) big=temp;  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        free_vector(xit,1,n); 
     vv[i]=1.0/big;        free_vector(xits,1,n); 
   }        free_vector(ptt,1,n); 
   for (j=1;j<=n;j++) {        free_vector(pt,1,n); 
     for (i=1;i<j;i++) {        return; 
       sum=a[i][j];      } 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       a[i][j]=sum;      for (j=1;j<=n;j++) { 
     }        ptt[j]=2.0*p[j]-pt[j]; 
     big=0.0;        xit[j]=p[j]-pt[j]; 
     for (i=j;i<=n;i++) {        pt[j]=p[j]; 
       sum=a[i][j];      } 
       for (k=1;k<j;k++)      fptt=(*func)(ptt); 
         sum -= a[i][k]*a[k][j];      if (fptt < fp) { 
       a[i][j]=sum;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       if ( (dum=vv[i]*fabs(sum)) >= big) {        if (t < 0.0) { 
         big=dum;          linmin(p,xit,n,fret,func); 
         imax=i;          for (j=1;j<=n;j++) { 
       }            xi[j][ibig]=xi[j][n]; 
     }            xi[j][n]=xit[j]; 
     if (j != imax) {          }
       for (k=1;k<=n;k++) {  #ifdef DEBUG
         dum=a[imax][k];          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         a[imax][k]=a[j][k];          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         a[j][k]=dum;          for(j=1;j<=n;j++){
       }            printf(" %.12e",xit[j]);
       *d = -(*d);            fprintf(ficlog," %.12e",xit[j]);
       vv[imax]=vv[j];          }
     }          printf("\n");
     indx[j]=imax;          fprintf(ficlog,"\n");
     if (a[j][j] == 0.0) a[j][j]=TINY;  #endif
     if (j != n) {        }
       dum=1.0/(a[j][j]);      } 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    } 
     }  } 
   }  
   free_vector(vv,1,n);  /* Doesn't work */  /**** Prevalence limit (stable or period prevalence)  ****************/
 ;  
 }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   {
 void lubksb(double **a, int n, int *indx, double b[])    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
 {       matrix by transitions matrix until convergence is reached */
   int i,ii=0,ip,j;  
   double sum;    int i, ii,j,k;
      double min, max, maxmin, maxmax,sumnew=0.;
   for (i=1;i<=n;i++) {    double **matprod2();
     ip=indx[i];    double **out, cov[NCOVMAX], **pmij();
     sum=b[ip];    double **newm;
     b[ip]=b[i];    double agefin, delaymax=50 ; /* Max number of years to converge */
     if (ii)  
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    for (ii=1;ii<=nlstate+ndeath;ii++)
     else if (sum) ii=i;      for (j=1;j<=nlstate+ndeath;j++){
     b[i]=sum;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }      }
   for (i=n;i>=1;i--) {  
     sum=b[i];     cov[1]=1.;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];   
     b[i]=sum/a[i][i];   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   }    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 }      newm=savm;
       /* Covariates have to be included here again */
 /************ Frequencies ********************/       cov[2]=agefin;
 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)    
 {  /* Some frequencies */        for (k=1; k<=cptcovn;k++) {
            cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          /*      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]]);*/
   double ***freq; /* Frequencies */        }
   double *pp;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double pos, k2, dateintsum=0,k2cpt=0;        for (k=1; k<=cptcovprod;k++)
   FILE *ficresp;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   char fileresp[FILENAMELENGTH];  
         /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   pp=vector(1,nlstate);        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   strcpy(fileresp,"p");      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   strcat(fileresp,fileres);  
   if((ficresp=fopen(fileresp,"w"))==NULL) {      savm=oldm;
     printf("Problem with prevalence resultfile: %s\n", fileresp);      oldm=newm;
     exit(0);      maxmax=0.;
   }      for(j=1;j<=nlstate;j++){
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        min=1.;
   j1=0;        max=0.;
         for(i=1; i<=nlstate; i++) {
   j=cptcoveff;          sumnew=0;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           prlim[i][j]= newm[i][j]/(1-sumnew);
   for(k1=1; k1<=j;k1++){          max=FMAX(max,prlim[i][j]);
    for(i1=1; i1<=ncodemax[k1];i1++){          min=FMIN(min,prlim[i][j]);
        j1++;        }
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        maxmin=max-min;
          scanf("%d", i);*/        maxmax=FMAX(maxmax,maxmin);
         for (i=-1; i<=nlstate+ndeath; i++)        }
          for (jk=-1; jk<=nlstate+ndeath; jk++)        if(maxmax < ftolpl){
            for(m=agemin; m <= agemax+3; m++)        return prlim;
              freq[i][jk][m]=0;      }
     }
         dateintsum=0;  }
         k2cpt=0;  
        for (i=1; i<=imx; i++) {  /*************** transition probabilities ***************/ 
          bool=1;  
          if  (cptcovn>0) {  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
            for (z1=1; z1<=cptcoveff; z1++)  {
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    double s1, s2;
                bool=0;    /*double t34;*/
          }    int i,j,j1, nc, ii, jj;
          if (bool==1) {  
            for(m=firstpass; m<=lastpass; m++){      for(i=1; i<= nlstate; i++){
              k2=anint[m][i]+(mint[m][i]/12.);        for(j=1; j<i;j++){
              if ((k2>=dateprev1) && (k2<=dateprev2)) {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
                if(agev[m][i]==0) agev[m][i]=agemax+1;            /*s2 += param[i][j][nc]*cov[nc];*/
                if(agev[m][i]==1) agev[m][i]=agemax+2;            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          }
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          ps[i][j]=s2;
                  dateintsum=dateintsum+k2;  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
                  k2cpt++;        }
                }        for(j=i+1; j<=nlstate+ndeath;j++){
           for (nc=1, s2=0.;nc <=ncovmodel; nc++){
              }            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
            }  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
          }          }
        }          ps[i][j]=s2;
         if  (cptcovn>0) {        }
          fprintf(ficresp, "\n#********** Variable ");      }
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      /*ps[3][2]=1;*/
        fprintf(ficresp, "**********\n#");      
         }      for(i=1; i<= nlstate; i++){
        for(i=1; i<=nlstate;i++)        s1=0;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        for(j=1; j<i; j++)
        fprintf(ficresp, "\n");          s1+=exp(ps[i][j]);
                for(j=i+1; j<=nlstate+ndeath; j++)
   for(i=(int)agemin; i <= (int)agemax+3; i++){          s1+=exp(ps[i][j]);
     if(i==(int)agemax+3)        ps[i][i]=1./(s1+1.);
       printf("Total");        for(j=1; j<i; j++)
     else          ps[i][j]= exp(ps[i][j])*ps[i][i];
       printf("Age %d", i);        for(j=i+1; j<=nlstate+ndeath; j++)
     for(jk=1; jk <=nlstate ; jk++){          ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         pp[jk] += freq[jk][m][i];      } /* end i */
     }      
     for(jk=1; jk <=nlstate ; jk++){      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(m=-1, pos=0; m <=0 ; m++)        for(jj=1; jj<= nlstate+ndeath; jj++){
         pos += freq[jk][m][i];          ps[ii][jj]=0;
       if(pp[jk]>=1.e-10)          ps[ii][ii]=1;
         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);      
     }  
   /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
      for(jk=1; jk <=nlstate ; jk++){  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  /*         printf("ddd %lf ",ps[ii][jj]); */
         pp[jk] += freq[jk][m][i];  /*       } */
      }  /*       printf("\n "); */
   /*        } */
     for(jk=1,pos=0; jk <=nlstate ; jk++)  /*        printf("\n ");printf("%lf ",cov[2]); */
       pos += pp[jk];         /*
     for(jk=1; jk <=nlstate ; jk++){        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       if(pos>=1.e-5)        goto end;*/
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      return ps;
       else  }
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  
       if( i <= (int) agemax){  /**************** Product of 2 matrices ******************/
         if(pos>=1.e-5){  
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
           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]);*/    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         }       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       else    /* in, b, out are matrice of pointers which should have been initialized 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);       before: only the contents of out is modified. The function returns
       }       a pointer to pointers identical to out */
     }    long i, j, k;
     for(jk=-1; jk <=nlstate+ndeath; jk++)    for(i=nrl; i<= nrh; i++)
       for(m=-1; m <=nlstate+ndeath; m++)      for(k=ncolol; k<=ncoloh; k++)
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     if(i <= (int) agemax)          out[i][k] +=in[i][j]*b[j][k];
       fprintf(ficresp,"\n");  
     printf("\n");    return out;
     }  }
     }  
  }  
   dateintmean=dateintsum/k2cpt;  /************* Higher Matrix Product ***************/
    
   fclose(ficresp);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  {
   free_vector(pp,1,nlstate);    /* Computes the transition matrix starting at age 'age' over 
        'nhstepm*hstepm*stepm' months (i.e. until
   /* End of Freq */       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
 }       nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
 /************ Prevalence ********************/       (typically every 2 years instead of every month which is too big 
 void prevalence(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 calagedate)       for the memory).
 {  /* Some frequencies */       Model is determined by parameters x and covariates have to be 
         included manually here. 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */       */
   double *pp;  
   double pos, k2;    int i, j, d, h, k;
     double **out, cov[NCOVMAX];
   pp=vector(1,nlstate);    double **newm;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
      /* Hstepm could be zero and should return the unit matrix */
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    for (i=1;i<=nlstate+ndeath;i++)
   j1=0;      for (j=1;j<=nlstate+ndeath;j++){
          oldm[i][j]=(i==j ? 1.0 : 0.0);
   j=cptcoveff;        po[i][j][0]=(i==j ? 1.0 : 0.0);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      }
      /* Even if hstepm = 1, at least one multiplication by the unit matrix */
  for(k1=1; k1<=j;k1++){    for(h=1; h <=nhstepm; h++){
     for(i1=1; i1<=ncodemax[k1];i1++){      for(d=1; d <=hstepm; d++){
       j1++;        newm=savm;
          /* Covariates have to be included here again */
       for (i=-1; i<=nlstate+ndeath; i++)          cov[1]=1.;
         for (jk=-1; jk<=nlstate+ndeath; jk++)          cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
           for(m=agemin; m <= agemax+3; m++)        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
             freq[i][jk][m]=0;        for (k=1; k<=cptcovage;k++)
                cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       for (i=1; i<=imx; i++) {        for (k=1; k<=cptcovprod;k++)
         bool=1;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         if  (cptcovn>0) {  
           for (z1=1; z1<=cptcoveff; z1++)  
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
               bool=0;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         }        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         if (bool==1) {                     pmij(pmmij,cov,ncovmodel,x,nlstate));
           for(m=firstpass; m<=lastpass; m++){        savm=oldm;
             k2=anint[m][i]+(mint[m][i]/12.);        oldm=newm;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      }
               if(agev[m][i]==0) agev[m][i]=agemax+1;      for(i=1; i<=nlstate+ndeath; i++)
               if(agev[m][i]==1) agev[m][i]=agemax+2;        for(j=1;j<=nlstate+ndeath;j++) {
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          po[i][j][h]=newm[i][j];
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];            /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
             }           */
           }        }
         }    } /* end h */
       }    return po;
        }
         for(i=(int)agemin; i <= (int)agemax+3; i++){  
           for(jk=1; jk <=nlstate ; jk++){  
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  /*************** log-likelihood *************/
               pp[jk] += freq[jk][m][i];  double func( double *x)
           }  {
           for(jk=1; jk <=nlstate ; jk++){    int i, ii, j, k, mi, d, kk;
             for(m=-1, pos=0; m <=0 ; m++)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
             pos += freq[jk][m][i];    double **out;
         }    double sw; /* Sum of weights */
            double lli; /* Individual log likelihood */
          for(jk=1; jk <=nlstate ; jk++){    int s1, s2;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    double bbh, survp;
              pp[jk] += freq[jk][m][i];    long ipmx;
          }    /*extern weight */
              /* We are differentiating ll according to initial status */
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
          for(jk=1; jk <=nlstate ; jk++){                printf(" %d\n",s[4][i]);
            if( i <= (int) agemax){    */
              if(pos>=1.e-5){    cov[1]=1.;
                probs[i][jk][j1]= pp[jk]/pos;  
              }    for(k=1; k<=nlstate; k++) ll[k]=0.;
            }  
          }    if(mle==1){
                for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   free_vector(pp,1,nlstate);            }
            for(d=0; d<dh[mi][i]; d++){
 }  /* End of Freq */            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 /************* Waves Concatenation ***************/            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[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)            }
 {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      Death is a valid wave (if date is known).            savm=oldm;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i            oldm=newm;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          } /* end mult */
      and mw[mi+1][i]. dh depends on stepm.        
      */          /*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.
   int i, mi, m;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;           * (in months) between two waves is not a multiple of stepm, we rounded to 
      double sum=0., jmean=0.;*/           * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
   int j, k=0,jk, ju, jl;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   double sum=0.;           * probability in order to take into account the bias as a fraction of the way
   jmin=1e+5;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   jmax=-1;           * -stepm/2 to stepm/2 .
   jmean=0.;           * For stepm=1 the results are the same as for previous versions of Imach.
   for(i=1; i<=imx; i++){           * For stepm > 1 the results are less biased than in previous versions. 
     mi=0;           */
     m=firstpass;          s1=s[mw[mi][i]][i];
     while(s[m][i] <= nlstate){          s2=s[mw[mi+1][i]][i];
       if(s[m][i]>=1)          bbh=(double)bh[mi][i]/(double)stepm; 
         mw[++mi][i]=m;          /* bias bh is positive if real duration
       if(m >=lastpass)           * is higher than the multiple of stepm and negative otherwise.
         break;           */
       else          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         m++;          if( s2 > nlstate){ 
     }/* end while */            /* i.e. if s2 is a death state and if the date of death is known 
     if (s[m][i] > nlstate){               then the contribution to the likelihood is the probability to 
       mi++;     /* Death is another wave */               die between last step unit time and current  step unit time, 
       /* if(mi==0)  never been interviewed correctly before death */               which is also equal to probability to die before dh 
          /* Only death is a correct wave */               minus probability to die before dh-stepm . 
       mw[mi][i]=m;               In version up to 0.92 likelihood was computed
     }          as if date of death was unknown. Death was treated as any other
           health state: the date of the interview describes the actual state
     wav[i]=mi;          and not the date of a change in health state. The former idea was
     if(mi==0)          to consider that at each interview the state was recorded
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          (healthy, disable or death) and IMaCh was corrected; but when we
   }          introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
   for(i=1; i<=imx; i++){          contribution is smaller and very dependent of the step unit
     for(mi=1; mi<wav[i];mi++){          stepm. It is no more the probability to die between last interview
       if (stepm <=0)          and month of death but the probability to survive from last
         dh[mi][i]=1;          interview up to one month before death multiplied by the
       else{          probability to die within a month. Thanks to Chris
         if (s[mw[mi+1][i]][i] > nlstate) {          Jackson for correcting this bug.  Former versions increased
           if (agedc[i] < 2*AGESUP) {          mortality artificially. The bad side is that we add another loop
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          which slows down the processing. The difference can be up to 10%
           if(j==0) j=1;  /* Survives at least one month after exam */          lower mortality.
           k=k+1;            */
           if (j >= jmax) jmax=j;            lli=log(out[s1][s2] - savm[s1][s2]);
           if (j <= jmin) jmin=j;  
           sum=sum+j;  
           /* if (j<10) printf("j=%d num=%d ",j,i); */          } else if  (s2==-2) {
           }            for (j=1,survp=0. ; j<=nlstate; j++) 
         }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         else{            /*survp += out[s1][j]; */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            lli= log(survp);
           k=k+1;          }
           if (j >= jmax) jmax=j;          
           else if (j <= jmin)jmin=j;          else if  (s2==-4) { 
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            for (j=3,survp=0. ; j<=nlstate; j++)  
           sum=sum+j;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         }            lli= log(survp); 
         jk= j/stepm;          } 
         jl= j -jk*stepm;  
         ju= j -(jk+1)*stepm;          else if  (s2==-5) { 
         if(jl <= -ju)            for (j=1,survp=0. ; j<=2; j++)  
           dh[mi][i]=jk;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         else            lli= log(survp); 
           dh[mi][i]=jk+1;          } 
         if(dh[mi][i]==0)          
           dh[mi][i]=1; /* At least one step */          else{
       }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   }          } 
   jmean=sum/k;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          /*if(lli ==000.0)*/
  }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
 /*********** Tricode ****************************/          ipmx +=1;
 void tricode(int *Tvar, int **nbcode, int imx)          sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int Ndum[20],ij=1, k, j, i;        } /* end of wave */
   int cptcode=0;      } /* end of individual */
   cptcoveff=0;    }  else if(mle==2){
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (k=0; k<19; k++) Ndum[k]=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (k=1; k<=7; k++) ncodemax[k]=0;        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {            for (j=1;j<=nlstate+ndeath;j++){
     for (i=1; i<=imx; i++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       ij=(int)(covar[Tvar[j]][i]);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       Ndum[ij]++;            }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          for(d=0; d<=dh[mi][i]; d++){
       if (ij > cptcode) cptcode=ij;            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     for (i=0; i<=cptcode; i++) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       if(Ndum[i]!=0) ncodemax[j]++;            }
     }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     ij=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
             oldm=newm;
     for (i=1; i<=ncodemax[j]; i++) {          } /* end mult */
       for (k=0; k<=19; k++) {        
         if (Ndum[k] != 0) {          s1=s[mw[mi][i]][i];
           nbcode[Tvar[j]][ij]=k;          s2=s[mw[mi+1][i]][i];
           ij++;          bbh=(double)bh[mi][i]/(double)stepm; 
         }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         if (ij > ncodemax[j]) break;          ipmx +=1;
       }            sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }          } /* end of wave */
       } /* end of individual */
  for (k=0; k<19; k++) Ndum[k]=0;    }  else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
  for (i=1; i<=ncovmodel-2; i++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       ij=Tvar[i];        for(mi=1; mi<= wav[i]-1; mi++){
       Ndum[ij]++;          for (ii=1;ii<=nlstate+ndeath;ii++)
     }            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  ij=1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
  for (i=1; i<=10; i++) {            }
    if((Ndum[i]!=0) && (i<=ncov)){          for(d=0; d<dh[mi][i]; d++){
      Tvaraff[ij]=i;            newm=savm;
      ij++;            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];
              }
     cptcoveff=ij-1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
 /*********** Health Expectancies ****************/            oldm=newm;
           } /* end mult */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        
 {          s1=s[mw[mi][i]][i];
   /* Health expectancies */          s2=s[mw[mi+1][i]][i];
   int i, j, nhstepm, hstepm, h;          bbh=(double)bh[mi][i]/(double)stepm; 
   double age, agelim,hf;          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 ***p3mat;          ipmx +=1;
            sw += weight[i];
   fprintf(ficreseij,"# Health expectancies\n");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   fprintf(ficreseij,"# Age");        } /* end of wave */
   for(i=1; i<=nlstate;i++)      } /* end of individual */
     for(j=1; j<=nlstate;j++)    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       fprintf(ficreseij," %1d-%1d",i,j);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   fprintf(ficreseij,"\n");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   hstepm=1*YEARM; /*  Every j years of age (in month) */          for (ii=1;ii<=nlstate+ndeath;ii++)
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   agelim=AGESUP;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            }
     /* nhstepm age range expressed in number of stepm */          for(d=0; d<dh[mi][i]; d++){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);            newm=savm;
     /* Typically if 20 years = 20*12/6=40 stepm */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     if (stepm >= YEARM) hstepm=1;            for (kk=1; kk<=cptcovage;kk++) {
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
             oldm=newm;
     for(i=1; i<=nlstate;i++)          } /* end mult */
       for(j=1; j<=nlstate;j++)        
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          s1=s[mw[mi][i]][i];
           eij[i][j][(int)age] +=p3mat[i][j][h];          s2=s[mw[mi+1][i]][i];
         }          if( s2 > nlstate){ 
                lli=log(out[s1][s2] - savm[s1][s2]);
     hf=1;          }else{
     if (stepm >= YEARM) hf=stepm/YEARM;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     fprintf(ficreseij,"%.0f",age );          }
     for(i=1; i<=nlstate;i++)          ipmx +=1;
       for(j=1; j<=nlstate;j++){          sw += weight[i];
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          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]); */
     fprintf(ficreseij,"\n");        } /* end of wave */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } /* end of individual */
   }    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
 }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 /************ Variance ******************/        for(mi=1; mi<= wav[i]-1; mi++){
 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)          for (ii=1;ii<=nlstate+ndeath;ii++)
 {            for (j=1;j<=nlstate+ndeath;j++){
   /* Variance of health expectancies */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **newm;            }
   double **dnewm,**doldm;          for(d=0; d<dh[mi][i]; d++){
   int i, j, nhstepm, hstepm, h;            newm=savm;
   int k, cptcode;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double *xp;            for (kk=1; kk<=cptcovage;kk++) {
   double **gp, **gm;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double ***gradg, ***trgradg;            }
   double ***p3mat;          
   double age,agelim;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int theta;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
    fprintf(ficresvij,"# Covariances of life expectancies\n");            oldm=newm;
   fprintf(ficresvij,"# Age");          } /* end mult */
   for(i=1; i<=nlstate;i++)        
     for(j=1; j<=nlstate;j++)          s1=s[mw[mi][i]][i];
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          s2=s[mw[mi+1][i]][i];
   fprintf(ficresvij,"\n");          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
   xp=vector(1,npar);          sw += weight[i];
   dnewm=matrix(1,nlstate,1,npar);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   doldm=matrix(1,nlstate,1,nlstate);          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
          } /* end of wave */
   hstepm=1*YEARM; /* Every year of age */      } /* end of individual */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    } /* End of if */
   agelim = AGESUP;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if (stepm >= YEARM) hstepm=1;    return -l;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  /*************** log-likelihood *************/
     gp=matrix(0,nhstepm,1,nlstate);  double funcone( double *x)
     gm=matrix(0,nhstepm,1,nlstate);  {
     /* Same as likeli but slower because of a lot of printf and if */
     for(theta=1; theta <=npar; theta++){    int i, ii, j, k, mi, d, kk;
       for(i=1; i<=npar; i++){ /* Computes gradient */    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double **out;
       }    double lli; /* Individual log likelihood */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      double llt;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int s1, s2;
     double bbh, survp;
       if (popbased==1) {    /*extern weight */
         for(i=1; i<=nlstate;i++)    /* We are differentiating ll according to initial status */
           prlim[i][i]=probs[(int)age][i][ij];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       }    /*for(i=1;i<imx;i++) 
            printf(" %d\n",s[4][i]);
       for(j=1; j<= nlstate; j++){    */
         for(h=0; h<=nhstepm; h++){    cov[1]=1.;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    for(k=1; k<=nlstate; k++) ll[k]=0.;
         }  
       }    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(i=1; i<=npar; i++) /* Computes gradient */      for(mi=1; mi<= wav[i]-1; mi++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        for (ii=1;ii<=nlstate+ndeath;ii++)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            for (j=1;j<=nlstate+ndeath;j++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);
       if (popbased==1) {          }
         for(i=1; i<=nlstate;i++)        for(d=0; d<dh[mi][i]; d++){
           prlim[i][i]=probs[(int)age][i][ij];          newm=savm;
       }          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
       for(j=1; j<= nlstate; j++){            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for(h=0; h<=nhstepm; h++){          }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }          savm=oldm;
       }          oldm=newm;
         } /* end mult */
       for(j=1; j<= nlstate; j++)        
         for(h=0; h<=nhstepm; h++){        s1=s[mw[mi][i]][i];
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        s2=s[mw[mi+1][i]][i];
         }        bbh=(double)bh[mi][i]/(double)stepm; 
     } /* End theta */        /* bias is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);         */
         if( s2 > nlstate && (mle <5) ){  /* Jackson */
     for(h=0; h<=nhstepm; h++)          lli=log(out[s1][s2] - savm[s1][s2]);
       for(j=1; j<=nlstate;j++)        } else if  (s2==-2) {
         for(theta=1; theta <=npar; theta++)          for (j=1,survp=0. ; j<=nlstate; j++) 
           trgradg[h][j][theta]=gradg[h][theta][j];            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);
     for(i=1;i<=nlstate;i++)        }else if (mle==1){
       for(j=1;j<=nlstate;j++)          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         vareij[i][j][(int)age] =0.;        } else if(mle==2){
     for(h=0;h<=nhstepm;h++){          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       for(k=0;k<=nhstepm;k++){        } else if(mle==3){  /* exponential inter-extrapolation */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          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 */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         for(i=1;i<=nlstate;i++)          lli=log(out[s1][s2]); /* Original formula */
           for(j=1;j<=nlstate;j++)        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
             vareij[i][j][(int)age] += doldm[i][j];          lli=log(out[s1][s2]); /* Original formula */
       }        } /* End of if */
     }        ipmx +=1;
     h=1;        sw += weight[i];
     if (stepm >= YEARM) h=stepm/YEARM;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     fprintf(ficresvij,"%.0f ",age );  /*       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(i=1; i<=nlstate;i++)        if(globpr){
       for(j=1; j<=nlstate;j++){          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);   %11.6f %11.6f %11.6f ", \
       }                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     fprintf(ficresvij,"\n");                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     free_matrix(gp,0,nhstepm,1,nlstate);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     free_matrix(gm,0,nhstepm,1,nlstate);            llt +=ll[k]*gipmx/gsw;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresilk," %10.6f\n", -llt);
   } /* End age */        }
        } /* end of wave */
   free_vector(xp,1,npar);    } /* end of individual */
   free_matrix(doldm,1,nlstate,1,npar);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   free_matrix(dnewm,1,nlstate,1,nlstate);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
 }    if(globpr==0){ /* First time we count the contributions and weights */
       gipmx=ipmx;
 /************ Variance of prevlim ******************/      gsw=sw;
 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)    }
 {    return -l;
   /* Variance of prevalence limit */  }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;  
   double **dnewm,**doldm;  /*************** function likelione ***********/
   int i, j, nhstepm, hstepm;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   int k, cptcode;  {
   double *xp;    /* This routine should help understanding what is done with 
   double *gp, *gm;       the selection of individuals/waves and
   double **gradg, **trgradg;       to check the exact contribution to the likelihood.
   double age,agelim;       Plotting could be done.
   int theta;     */
        int k;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");  
   fprintf(ficresvpl,"# Age");    if(*globpri !=0){ /* Just counts and sums, no printings */
   for(i=1; i<=nlstate;i++)      strcpy(fileresilk,"ilk"); 
       fprintf(ficresvpl," %1d-%1d",i,i);      strcat(fileresilk,fileres);
   fprintf(ficresvpl,"\n");      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
   xp=vector(1,npar);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   dnewm=matrix(1,nlstate,1,npar);      }
   doldm=matrix(1,nlstate,1,nlstate);      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
        fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   hstepm=1*YEARM; /* Every year of age */      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      for(k=1; k<=nlstate; k++) 
   agelim = AGESUP;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    }
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    *fretone=(*funcone)(p);
     gradg=matrix(1,npar,1,nlstate);    if(*globpri !=0){
     gp=vector(1,nlstate);      fclose(ficresilk);
     gm=vector(1,nlstate);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fflush(fichtm); 
     for(theta=1; theta <=npar; theta++){    } 
       for(i=1; i<=npar; i++){ /* Computes gradient */    return;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  }
       }  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)  /*********** Maximum Likelihood Estimation ***************/
         gp[i] = prlim[i][i];  
      void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       for(i=1; i<=npar; i++) /* Computes gradient */  {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    int i,j, iter;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double **xi;
       for(i=1;i<=nlstate;i++)    double fret;
         gm[i] = prlim[i][i];    double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
       for(i=1;i<=nlstate;i++)    xi=matrix(1,npar,1,npar);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    for (i=1;i<=npar;i++)
     } /* End theta */      for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
     trgradg =matrix(1,nlstate,1,npar);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
     for(j=1; j<=nlstate;j++)    strcat(filerespow,fileres);
       for(theta=1; theta <=npar; theta++)    if((ficrespow=fopen(filerespow,"w"))==NULL) {
         trgradg[j][theta]=gradg[theta][j];      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     for(i=1;i<=nlstate;i++)    }
       varpl[i][(int)age] =0.;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    for (i=1;i<=nlstate;i++)
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      for(j=1;j<=nlstate+ndeath;j++)
     for(i=1;i<=nlstate;i++)        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    fprintf(ficrespow,"\n");
   
     fprintf(ficresvpl,"%.0f ",age );    powell(p,xi,npar,ftol,&iter,&fret,func);
     for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    free_matrix(xi,1,npar,1,npar);
     fprintf(ficresvpl,"\n");    fclose(ficrespow);
     free_vector(gp,1,nlstate);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     free_vector(gm,1,nlstate);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     free_matrix(gradg,1,npar,1,nlstate);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     free_matrix(trgradg,1,nlstate,1,npar);  
   } /* End age */  }
   
   free_vector(xp,1,npar);  /**** Computes Hessian and covariance matrix ***/
   free_matrix(doldm,1,nlstate,1,npar);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   free_matrix(dnewm,1,nlstate,1,nlstate);  {
     double  **a,**y,*x,pd;
 }    double **hess;
     int i, j,jk;
 /************ Variance of one-step probabilities  ******************/    int *indx;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)  
 {    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   int i, j;    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   int k=0, cptcode;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   double **dnewm,**doldm;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   double *xp;    double gompertz(double p[]);
   double *gp, *gm;    hess=matrix(1,npar,1,npar);
   double **gradg, **trgradg;  
   double age,agelim, cov[NCOVMAX];    printf("\nCalculation of the hessian matrix. Wait...\n");
   int theta;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   char fileresprob[FILENAMELENGTH];    for (i=1;i<=npar;i++){
       printf("%d",i);fflush(stdout);
   strcpy(fileresprob,"prob");      fprintf(ficlog,"%d",i);fflush(ficlog);
   strcat(fileresprob,fileres);     
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     printf("Problem with resultfile: %s\n", fileresprob);      
   }      /*  printf(" %f ",p[i]);
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
      }
     
   xp=vector(1,npar);    for (i=1;i<=npar;i++) {
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      for (j=1;j<=npar;j++)  {
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));        if (j>i) { 
            printf(".%d%d",i,j);fflush(stdout);
   cov[1]=1;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   for (age=bage; age<=fage; age ++){          hess[i][j]=hessij(p,delti,i,j,func,npar);
     cov[2]=age;          
     gradg=matrix(1,npar,1,9);          hess[j][i]=hess[i][j];    
     trgradg=matrix(1,9,1,npar);          /*printf(" %lf ",hess[i][j]);*/
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        }
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      }
        }
     for(theta=1; theta <=npar; theta++){    printf("\n");
       for(i=1; i<=npar; i++)    fprintf(ficlog,"\n");
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
          printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
        
       k=0;    a=matrix(1,npar,1,npar);
       for(i=1; i<= (nlstate+ndeath); i++){    y=matrix(1,npar,1,npar);
         for(j=1; j<=(nlstate+ndeath);j++){    x=vector(1,npar);
            k=k+1;    indx=ivector(1,npar);
           gp[k]=pmmij[i][j];    for (i=1;i<=npar;i++)
         }      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       }    ludcmp(a,npar,indx,&pd);
   
       for(i=1; i<=npar; i++)    for (j=1;j<=npar;j++) {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (i=1;i<=npar;i++) x[i]=0;
          x[j]=1;
       lubksb(a,npar,indx,x);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      for (i=1;i<=npar;i++){ 
       k=0;        matcov[i][j]=x[i];
       for(i=1; i<=(nlstate+ndeath); i++){      }
         for(j=1; j<=(nlstate+ndeath);j++){    }
           k=k+1;  
           gm[k]=pmmij[i][j];    printf("\n#Hessian matrix#\n");
         }    fprintf(ficlog,"\n#Hessian matrix#\n");
       }    for (i=1;i<=npar;i++) { 
            for (j=1;j<=npar;j++) { 
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        printf("%.3e ",hess[i][j]);
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          fprintf(ficlog,"%.3e ",hess[i][j]);
     }      }
       printf("\n");
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)      fprintf(ficlog,"\n");
       for(theta=1; theta <=npar; theta++)    }
       trgradg[j][theta]=gradg[theta][j];  
      /* Recompute Inverse */
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    for (i=1;i<=npar;i++)
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
      pmij(pmmij,cov,ncovmodel,x,nlstate);  
     /*  printf("\n#Hessian matrix recomputed#\n");
      k=0;  
      for(i=1; i<=(nlstate+ndeath); i++){    for (j=1;j<=npar;j++) {
        for(j=1; j<=(nlstate+ndeath);j++){      for (i=1;i<=npar;i++) x[i]=0;
          k=k+1;      x[j]=1;
          gm[k]=pmmij[i][j];      lubksb(a,npar,indx,x);
         }      for (i=1;i<=npar;i++){ 
      }        y[i][j]=x[i];
              printf("%.3e ",y[i][j]);
      /*printf("\n%d ",(int)age);        fprintf(ficlog,"%.3e ",y[i][j]);
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      }
              printf("\n");
       fprintf(ficlog,"\n");
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    }
      }*/    */
   
   fprintf(ficresprob,"\n%d ",(int)age);    free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    free_vector(x,1,npar);
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    free_ivector(indx,1,npar);
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    free_matrix(hess,1,npar,1,npar);
   }  
   
     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);  /*************** hessian matrix ****************/
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 }  {
  free_vector(xp,1,npar);    int i;
 fclose(ficresprob);    int l=1, lmax=20;
  exit(0);    double k1,k2;
 }    double p2[NPARMAX+1];
     double res;
 /***********************************************/    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
 /**************** Main Program *****************/    double fx;
 /***********************************************/    int k=0,kmax=10;
     double l1;
 int main(int argc, char *argv[])  
 {    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    for(l=0 ; l <=lmax; l++){
   double agedeb, agefin,hf;      l1=pow(10,l);
   double agemin=1.e20, agemax=-1.e20;      delts=delt;
       for(k=1 ; k <kmax; k=k+1){
   double fret;        delt = delta*(l1*k);
   double **xi,tmp,delta;        p2[theta]=x[theta] +delt;
         k1=func(p2)-fx;
   double dum; /* Dummy variable */        p2[theta]=x[theta]-delt;
   double ***p3mat;        k2=func(p2)-fx;
   int *indx;        /*res= (k1-2.0*fx+k2)/delt/delt; */
   char line[MAXLINE], linepar[MAXLINE];        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   char title[MAXLINE];        
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  #ifdef DEBUG
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];        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);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];  #endif
         /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   char filerest[FILENAMELENGTH];        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   char fileregp[FILENAMELENGTH];          k=kmax;
   char popfile[FILENAMELENGTH];        }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   int firstobs=1, lastobs=10;          k=kmax; l=lmax*10.;
   int sdeb, sfin; /* Status at beginning and end */        }
   int c,  h , cpt,l;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   int ju,jl, mi;          delts=delt;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        }
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      }
   int mobilav=0,popforecast=0;    }
   int hstepm, nhstepm;    delti[theta]=delts;
   int *popage;/*boolprev=0 if date and zero if wave*/    return res; 
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;    
   }
   double bage, fage, age, agelim, agebase;  
   double ftolpl=FTOL;  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   double **prlim;  {
   double *severity;    int i;
   double ***param; /* Matrix of parameters */    int l=1, l1, lmax=20;
   double  *p;    double k1,k2,k3,k4,res,fx;
   double **matcov; /* Matrix of covariance */    double p2[NPARMAX+1];
   double ***delti3; /* Scale */    int k;
   double *delti; /* Scale */  
   double ***eij, ***vareij;    fx=func(x);
   double **varpl; /* Variances of prevalence limits by age */    for (k=1; k<=2; k++) {
   double *epj, vepp;      for (i=1;i<=npar;i++) p2[i]=x[i];
   double kk1, kk2;      p2[thetai]=x[thetai]+delti[thetai]/k;
   double *popeffectif,*popcount;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;      k1=func(p2)-fx;
   double yp,yp1,yp2;    
       p2[thetai]=x[thetai]+delti[thetai]/k;
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   char *alph[]={"a","a","b","c","d","e"}, str[4];      k2=func(p2)-fx;
     
       p2[thetai]=x[thetai]-delti[thetai]/k;
   char z[1]="c", occ;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 #include <sys/time.h>      k3=func(p2)-fx;
 #include <time.h>    
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      p2[thetai]=x[thetai]-delti[thetai]/k;
        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   /* long total_usecs;      k4=func(p2)-fx;
   struct timeval start_time, end_time;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
    #ifdef DEBUG
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      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);
   #endif
   printf("\n%s",version);    }
   if(argc <=1){    return res;
     printf("\nEnter the parameter file name: ");  }
     scanf("%s",pathtot);  
   }  /************** Inverse of matrix **************/
   else{  void ludcmp(double **a, int n, int *indx, double *d) 
     strcpy(pathtot,argv[1]);  { 
   }    int i,imax,j,k; 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    double big,dum,sum,temp; 
   /*cygwin_split_path(pathtot,path,optionfile);    double *vv; 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/   
   /* cutv(path,optionfile,pathtot,'\\');*/    vv=vector(1,n); 
     *d=1.0; 
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    for (i=1;i<=n;i++) { 
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      big=0.0; 
   chdir(path);      for (j=1;j<=n;j++) 
   replace(pathc,path);        if ((temp=fabs(a[i][j])) > big) big=temp; 
       if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 /*-------- arguments in the command line --------*/      vv[i]=1.0/big; 
     } 
   strcpy(fileres,"r");    for (j=1;j<=n;j++) { 
   strcat(fileres, optionfilefiname);      for (i=1;i<j;i++) { 
   strcat(fileres,".txt");    /* Other files have txt extension */        sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   /*---------arguments file --------*/        a[i][j]=sum; 
       } 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      big=0.0; 
     printf("Problem with optionfile %s\n",optionfile);      for (i=j;i<=n;i++) { 
     goto end;        sum=a[i][j]; 
   }        for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
   strcpy(filereso,"o");        a[i][j]=sum; 
   strcat(filereso,fileres);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   if((ficparo=fopen(filereso,"w"))==NULL) {          big=dum; 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;          imax=i; 
   }        } 
       } 
   /* Reads comments: lines beginning with '#' */      if (j != imax) { 
   while((c=getc(ficpar))=='#' && c!= EOF){        for (k=1;k<=n;k++) { 
     ungetc(c,ficpar);          dum=a[imax][k]; 
     fgets(line, MAXLINE, ficpar);          a[imax][k]=a[j][k]; 
     puts(line);          a[j][k]=dum; 
     fputs(line,ficparo);        } 
   }        *d = -(*d); 
   ungetc(c,ficpar);        vv[imax]=vv[j]; 
       } 
   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);      indx[j]=imax; 
   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);      if (a[j][j] == 0.0) a[j][j]=TINY; 
   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 (j != n) { 
 while((c=getc(ficpar))=='#' && c!= EOF){        dum=1.0/(a[j][j]); 
     ungetc(c,ficpar);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     fgets(line, MAXLINE, ficpar);      } 
     puts(line);    } 
     fputs(line,ficparo);    free_vector(vv,1,n);  /* Doesn't work */
   }  ;
   ungetc(c,ficpar);  } 
    
      void lubksb(double **a, int n, int *indx, double b[]) 
   covar=matrix(0,NCOVMAX,1,n);  { 
   cptcovn=0;    int i,ii=0,ip,j; 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    double sum; 
    
   ncovmodel=2+cptcovn;    for (i=1;i<=n;i++) { 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      ip=indx[i]; 
        sum=b[ip]; 
   /* Read guess parameters */      b[ip]=b[i]; 
   /* Reads comments: lines beginning with '#' */      if (ii) 
   while((c=getc(ficpar))=='#' && c!= EOF){        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     ungetc(c,ficpar);      else if (sum) ii=i; 
     fgets(line, MAXLINE, ficpar);      b[i]=sum; 
     puts(line);    } 
     fputs(line,ficparo);    for (i=n;i>=1;i--) { 
   }      sum=b[i]; 
   ungetc(c,ficpar);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
        b[i]=sum/a[i][i]; 
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    } 
     for(i=1; i <=nlstate; i++)  } 
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);  void pstamp(FILE *fichier)
       fprintf(ficparo,"%1d%1d",i1,j1);  {
       printf("%1d%1d",i,j);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
       for(k=1; k<=ncovmodel;k++){  }
         fscanf(ficpar," %lf",&param[i][j][k]);  
         printf(" %lf",param[i][j][k]);  /************ Frequencies ********************/
         fprintf(ficparo," %lf",param[i][j][k]);  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
       }  {  /* Some frequencies */
       fscanf(ficpar,"\n");    
       printf("\n");    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       fprintf(ficparo,"\n");    int first;
     }    double ***freq; /* Frequencies */
      double *pp, **prop;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     char fileresp[FILENAMELENGTH];
   p=param[1][1];    
      pp=vector(1,nlstate);
   /* Reads comments: lines beginning with '#' */    prop=matrix(1,nlstate,iagemin,iagemax+3);
   while((c=getc(ficpar))=='#' && c!= EOF){    strcpy(fileresp,"p");
     ungetc(c,ficpar);    strcat(fileresp,fileres);
     fgets(line, MAXLINE, ficpar);    if((ficresp=fopen(fileresp,"w"))==NULL) {
     puts(line);      printf("Problem with prevalence resultfile: %s\n", fileresp);
     fputs(line,ficparo);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   }      exit(0);
   ungetc(c,ficpar);    }
     freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    j1=0;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    
   for(i=1; i <=nlstate; i++){    j=cptcoveff;
     for(j=1; j <=nlstate+ndeath-1; j++){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);    first=1;
       fprintf(ficparo,"%1d%1d",i1,j1);  
       for(k=1; k<=ncovmodel;k++){    for(k1=1; k1<=j;k1++){
         fscanf(ficpar,"%le",&delti3[i][j][k]);      for(i1=1; i1<=ncodemax[k1];i1++){
         printf(" %le",delti3[i][j][k]);        j1++;
         fprintf(ficparo," %le",delti3[i][j][k]);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       }          scanf("%d", i);*/
       fscanf(ficpar,"\n");        for (i=-5; i<=nlstate+ndeath; i++)  
       printf("\n");          for (jk=-5; jk<=nlstate+ndeath; jk++)  
       fprintf(ficparo,"\n");            for(m=iagemin; m <= iagemax+3; m++)
     }              freq[i][jk][m]=0;
   }  
   delti=delti3[1][1];      for (i=1; i<=nlstate; i++)  
          for(m=iagemin; m <= iagemax+3; m++)
   /* Reads comments: lines beginning with '#' */          prop[i][m]=0;
   while((c=getc(ficpar))=='#' && c!= EOF){        
     ungetc(c,ficpar);        dateintsum=0;
     fgets(line, MAXLINE, ficpar);        k2cpt=0;
     puts(line);        for (i=1; i<=imx; i++) {
     fputs(line,ficparo);          bool=1;
   }          if  (cptcovn>0) {
   ungetc(c,ficpar);            for (z1=1; z1<=cptcoveff; z1++) 
                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   matcov=matrix(1,npar,1,npar);                bool=0;
   for(i=1; i <=npar; i++){          }
     fscanf(ficpar,"%s",&str);          if (bool==1){
     printf("%s",str);            for(m=firstpass; m<=lastpass; m++){
     fprintf(ficparo,"%s",str);              k2=anint[m][i]+(mint[m][i]/12.);
     for(j=1; j <=i; j++){              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       fscanf(ficpar," %le",&matcov[i][j]);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       printf(" %.5le",matcov[i][j]);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       fprintf(ficparo," %.5le",matcov[i][j]);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     }                if (m<lastpass) {
     fscanf(ficpar,"\n");                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     printf("\n");                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     fprintf(ficparo,"\n");                }
   }                
   for(i=1; i <=npar; i++)                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     for(j=i+1;j<=npar;j++)                  dateintsum=dateintsum+k2;
       matcov[i][j]=matcov[j][i];                  k2cpt++;
                    }
   printf("\n");                /*}*/
             }
           }
     /*-------- data file ----------*/        }
     if((ficres =fopen(fileres,"w"))==NULL) {         
       printf("Problem with resultfile: %s\n", fileres);goto end;        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     }        pstamp(ficresp);
     fprintf(ficres,"#%s\n",version);        if  (cptcovn>0) {
              fprintf(ficresp, "\n#********** Variable "); 
     if((fic=fopen(datafile,"r"))==NULL)    {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       printf("Problem with datafile: %s\n", datafile);goto end;          fprintf(ficresp, "**********\n#");
     }        }
         for(i=1; i<=nlstate;i++) 
     n= lastobs;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     severity = vector(1,maxwav);        fprintf(ficresp, "\n");
     outcome=imatrix(1,maxwav+1,1,n);        
     num=ivector(1,n);        for(i=iagemin; i <= iagemax+3; i++){
     moisnais=vector(1,n);          if(i==iagemax+3){
     annais=vector(1,n);            fprintf(ficlog,"Total");
     moisdc=vector(1,n);          }else{
     andc=vector(1,n);            if(first==1){
     agedc=vector(1,n);              first=0;
     cod=ivector(1,n);              printf("See log file for details...\n");
     weight=vector(1,n);            }
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */            fprintf(ficlog,"Age %d", i);
     mint=matrix(1,maxwav,1,n);          }
     anint=matrix(1,maxwav,1,n);          for(jk=1; jk <=nlstate ; jk++){
     s=imatrix(1,maxwav+1,1,n);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     adl=imatrix(1,maxwav+1,1,n);                  pp[jk] += freq[jk][m][i]; 
     tab=ivector(1,NCOVMAX);          }
     ncodemax=ivector(1,8);          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
     i=1;              pos += freq[jk][m][i];
     while (fgets(line, MAXLINE, fic) != NULL)    {            if(pp[jk]>=1.e-10){
       if ((i >= firstobs) && (i <=lastobs)) {              if(first==1){
                      printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         for (j=maxwav;j>=1;j--){              }
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           strcpy(line,stra);            }else{
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              if(first==1)
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                    }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);          }
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  
           for(jk=1; jk <=nlstate ; jk++){
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);              pp[jk] += freq[jk][m][i];
           }       
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
         for (j=ncov;j>=1;j--){            pos += pp[jk];
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);            posprop += prop[jk][i];
         }          }
         num[i]=atol(stra);          for(jk=1; jk <=nlstate ; jk++){
                    if(pos>=1.e-5){
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){              if(first==1)
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         i=i+1;            }else{
       }              if(first==1)
     }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     /* printf("ii=%d", ij);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
        scanf("%d",i);*/            }
   imx=i-1; /* Number of individuals */            if( i <= iagemax){
               if(pos>=1.e-5){
   /* for (i=1; i<=imx; i++){                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;                /*probs[i][jk][j1]= pp[jk]/pos;*/
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;              }
     }              else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     for (i=1; i<=imx; i++)            }
     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*/          for(jk=-1; jk <=nlstate+ndeath; jk++)
   Tvar=ivector(1,15);            for(m=-1; m <=nlstate+ndeath; m++)
   Tprod=ivector(1,15);              if(freq[jk][m][i] !=0 ) {
   Tvaraff=ivector(1,15);              if(first==1)
   Tvard=imatrix(1,15,1,2);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   Tage=ivector(1,15);                      fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                  }
   if (strlen(model) >1){          if(i <= iagemax)
     j=0, j1=0, k1=1, k2=1;            fprintf(ficresp,"\n");
     j=nbocc(model,'+');          if(first==1)
     j1=nbocc(model,'*');            printf("Others in log...\n");
     cptcovn=j+1;          fprintf(ficlog,"\n");
     cptcovprod=j1;        }
          }
        }
     strcpy(modelsav,model);    dateintmean=dateintsum/k2cpt; 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){   
       printf("Error. Non available option model=%s ",model);    fclose(ficresp);
       goto end;    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     }    free_vector(pp,1,nlstate);
        free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     for(i=(j+1); i>=1;i--){    /* End of Freq */
       cutv(stra,strb,modelsav,'+');  }
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  /************ Prevalence ********************/
       /*scanf("%d",i);*/  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)
       if (strchr(strb,'*')) {  {  
         cutv(strd,strc,strb,'*');    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         if (strcmp(strc,"age")==0) {       in each health status at the date of interview (if between dateprev1 and dateprev2).
           cptcovprod--;       We still use firstpass and lastpass as another selection.
           cutv(strb,stre,strd,'V');    */
           Tvar[i]=atoi(stre);   
           cptcovage++;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
             Tage[cptcovage]=i;    double ***freq; /* Frequencies */
             /*printf("stre=%s ", stre);*/    double *pp, **prop;
         }    double pos,posprop; 
         else if (strcmp(strd,"age")==0) {    double  y2; /* in fractional years */
           cptcovprod--;    int iagemin, iagemax;
           cutv(strb,stre,strc,'V');  
           Tvar[i]=atoi(stre);    iagemin= (int) agemin;
           cptcovage++;    iagemax= (int) agemax;
           Tage[cptcovage]=i;    /*pp=vector(1,nlstate);*/
         }    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         else {    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
           cutv(strb,stre,strc,'V');    j1=0;
           Tvar[i]=ncov+k1;    
           cutv(strb,strc,strd,'V');    j=cptcoveff;
           Tprod[k1]=i;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           Tvard[k1][1]=atoi(strc);    
           Tvard[k1][2]=atoi(stre);    for(k1=1; k1<=j;k1++){
           Tvar[cptcovn+k2]=Tvard[k1][1];      for(i1=1; i1<=ncodemax[k1];i1++){
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        j1++;
           for (k=1; k<=lastobs;k++)        
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        for (i=1; i<=nlstate; i++)  
           k1++;          for(m=iagemin; m <= iagemax+3; m++)
           k2=k2+2;            prop[i][m]=0.0;
         }       
       }        for (i=1; i<=imx; i++) { /* Each individual */
       else {          bool=1;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          if  (cptcovn>0) {
        /*  scanf("%d",i);*/            for (z1=1; z1<=cptcoveff; z1++) 
       cutv(strd,strc,strb,'V');              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       Tvar[i]=atoi(strc);                bool=0;
       }          } 
       strcpy(modelsav,stra);            if (bool==1) { 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
         scanf("%d",i);*/              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     }              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
 }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                  if(agev[m][i]==1) agev[m][i]=iagemax+2;
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                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); 
   printf("cptcovprod=%d ", cptcovprod);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   scanf("%d ",i);*/                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
     fclose(fic);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
     /*  if(mle==1){*/                } 
     if (weightopt != 1) { /* Maximisation without weights*/              }
       for(i=1;i<=n;i++) weight[i]=1.0;            } /* end selection of waves */
     }          }
     /*-calculation of age at interview from date of interview and age at death -*/        }
     agev=matrix(1,maxwav,1,imx);        for(i=iagemin; i <= iagemax+3; i++){  
           
    for (i=1; i<=imx; i++)          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
      for(m=2; (m<= maxwav); m++)            posprop += prop[jk][i]; 
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          } 
          anint[m][i]=9999;  
          s[m][i]=-1;          for(jk=1; jk <=nlstate ; jk++){     
        }            if( i <=  iagemax){ 
                  if(posprop>=1.e-5){ 
     for (i=1; i<=imx; i++)  {                probs[i][jk][j1]= prop[jk][i]/posprop;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);              } 
       for(m=1; (m<= maxwav); m++){            } 
         if(s[m][i] >0){          }/* end jk */ 
           if (s[m][i] == nlstate+1) {        }/* end i */ 
             if(agedc[i]>0)      } /* end i1 */
               if(moisdc[i]!=99 && andc[i]!=9999)    } /* end k1 */
               agev[m][i]=agedc[i];    
             else {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
               if (andc[i]!=9999){    /*free_vector(pp,1,nlstate);*/
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
               agev[m][i]=-1;  }  /* End of prevalence */
               }  
             }  /************* Waves Concatenation ***************/
           }  
           else if(s[m][i] !=9){ /* Should no more exist */  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)
             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)    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
               agev[m][i]=1;       Death is a valid wave (if date is known).
             else if(agev[m][i] <agemin){       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
               agemin=agev[m][i];       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/       and mw[mi+1][i]. dh depends on stepm.
             }       */
             else if(agev[m][i] >agemax){  
               agemax=agev[m][i];    int i, mi, m;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
             }       double sum=0., jmean=0.;*/
             /*agev[m][i]=anint[m][i]-annais[i];*/    int first;
             /*   agev[m][i] = age[i]+2*m;*/    int j, k=0,jk, ju, jl;
           }    double sum=0.;
           else { /* =9 */    first=0;
             agev[m][i]=1;    jmin=1e+5;
             s[m][i]=-1;    jmax=-1;
           }    jmean=0.;
         }    for(i=1; i<=imx; i++){
         else /*= 0 Unknown */      mi=0;
           agev[m][i]=1;      m=firstpass;
       }      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;
     for (i=1; i<=imx; i++)  {        if(m >=lastpass)
       for(m=1; (m<= maxwav); m++){          break;
         if (s[m][i] > (nlstate+ndeath)) {        else
           printf("Error: Wrong value in nlstate or ndeath\n");            m++;
           goto end;      }/* end while */
         }      if (s[m][i] > nlstate){
       }        mi++;     /* Death is another wave */
     }        /* if(mi==0)  never been interviewed correctly before death */
            /* Only death is a correct wave */
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        mw[mi][i]=m;
       }
     free_vector(severity,1,maxwav);  
     free_imatrix(outcome,1,maxwav+1,1,n);      wav[i]=mi;
     free_vector(moisnais,1,n);      if(mi==0){
     free_vector(annais,1,n);        nbwarn++;
     /* free_matrix(mint,1,maxwav,1,n);        if(first==0){
        free_matrix(anint,1,maxwav,1,n);*/          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     free_vector(moisdc,1,n);          first=1;
     free_vector(andc,1,n);        }
         if(first==1){
              fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
     wav=ivector(1,imx);        }
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      } /* end mi==0 */
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    } /* End individuals */
      
     /* Concatenates waves */    for(i=1; i<=imx; i++){
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      for(mi=1; mi<wav[i];mi++){
         if (stepm <=0)
           dh[mi][i]=1;
       Tcode=ivector(1,100);        else{
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       ncodemax[1]=1;            if (agedc[i] < 2*AGESUP) {
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                    if(j==0) j=1;  /* Survives at least one month after exam */
    codtab=imatrix(1,100,1,10);              else if(j<0){
    h=0;                nberr++;
    m=pow(2,cptcoveff);                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]);
                  j=1; /* Temporary Dangerous patch */
    for(k=1;k<=cptcoveff; k++){                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
      for(i=1; i <=(m/pow(2,k));i++){                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
        for(j=1; j <= ncodemax[k]; j++){                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){              }
            h++;              k=k+1;
            if (h>m) h=1;codtab[h][k]=j;              if (j >= jmax){
          }                jmax=j;
        }                ijmax=i;
      }              }
    }              if (j <= jmin){
                 jmin=j;
                 ijmin=i;
    /*for(i=1; i <=m ;i++){              }
      for(k=1; k <=cptcovn; k++){              sum=sum+j;
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
      }              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
      printf("\n");            }
    }          }
    scanf("%d",i);*/          else{
                j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
    /* Calculates basic frequencies. Computes observed prevalence at single age  /*        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]); */
        and prints on file fileres'p'. */  
             k=k+1;
                if (j >= jmax) {
                  jmax=j;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              ijmax=i;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            }
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            else if (j <= jmin){
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              jmin=j;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              ijmin=i;
                  }
     /* For Powell, parameters are in a vector p[] starting at p[1]            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */            /*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]);*/
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */            if(j<0){
               nberr++;
     if(mle==1){              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]);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);              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]);
     }            }
                sum=sum+j;
     /*--------- results files --------------*/          }
     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=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);          jk= j/stepm;
            jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
    jk=1;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
    fprintf(ficres,"# Parameters\n");            if(jl==0){
    printf("# Parameters\n");              dh[mi][i]=jk;
    for(i=1,jk=1; i <=nlstate; i++){              bh[mi][i]=0;
      for(k=1; k <=(nlstate+ndeath); k++){            }else{ /* We want a negative bias in order to only have interpolation ie
        if (k != i)                    * at the price of an extra matrix product in likelihood */
          {              dh[mi][i]=jk+1;
            printf("%d%d ",i,k);              bh[mi][i]=ju;
            fprintf(ficres,"%1d%1d ",i,k);            }
            for(j=1; j <=ncovmodel; j++){          }else{
              printf("%f ",p[jk]);            if(jl <= -ju){
              fprintf(ficres,"%f ",p[jk]);              dh[mi][i]=jk;
              jk++;              bh[mi][i]=jl;       /* bias is positive if real duration
            }                                   * is higher than the multiple of stepm and negative otherwise.
            printf("\n");                                   */
            fprintf(ficres,"\n");            }
          }            else{
      }              dh[mi][i]=jk+1;
    }              bh[mi][i]=ju;
  if(mle==1){            }
     /* Computing hessian and covariance matrix */            if(dh[mi][i]==0){
     ftolhess=ftol; /* Usually correct */              dh[mi][i]=1; /* At least one step */
     hesscov(matcov, p, npar, delti, ftolhess, func);              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);*/
     fprintf(ficres,"# Scales\n");            }
     printf("# Scales\n");          } /* end if mle */
      for(i=1,jk=1; i <=nlstate; i++){        }
       for(j=1; j <=nlstate+ndeath; j++){      } /* end wave */
         if (j!=i) {    }
           fprintf(ficres,"%1d%1d",i,j);    jmean=sum/k;
           printf("%1d%1d",i,j);    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
           for(k=1; k<=ncovmodel;k++){    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(" %.5e",delti[jk]);   }
             fprintf(ficres," %.5e",delti[jk]);  
             jk++;  /*********** Tricode ****************************/
           }  void tricode(int *Tvar, int **nbcode, int imx)
           printf("\n");  {
           fprintf(ficres,"\n");    
         }    int Ndum[20],ij=1, k, j, i, maxncov=19;
       }    int cptcode=0;
      }    cptcoveff=0; 
       
     k=1;    for (k=0; k<maxncov; k++) Ndum[k]=0;
     fprintf(ficres,"# Covariance\n");    for (k=1; k<=7; k++) ncodemax[k]=0;
     printf("# Covariance\n");  
     for(i=1;i<=npar;i++){    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       /*  if (k>nlstate) k=1;      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
       i1=(i-1)/(ncovmodel*nlstate)+1;                                 modality*/ 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
       printf("%s%d%d",alph[k],i1,tab[i]);*/        Ndum[ij]++; /*store the modality */
       fprintf(ficres,"%3d",i);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       printf("%3d",i);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
       for(j=1; j<=i;j++){                                         Tvar[j]. If V=sex and male is 0 and 
         fprintf(ficres," %.5e",matcov[i][j]);                                         female is 1, then  cptcode=1.*/
         printf(" %.5e",matcov[i][j]);      }
       }  
       fprintf(ficres,"\n");      for (i=0; i<=cptcode; i++) {
       printf("\n");        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
       k++;      }
     }  
          ij=1; 
     while((c=getc(ficpar))=='#' && c!= EOF){      for (i=1; i<=ncodemax[j]; i++) {
       ungetc(c,ficpar);        for (k=0; k<= maxncov; k++) {
       fgets(line, MAXLINE, ficpar);          if (Ndum[k] != 0) {
       puts(line);            nbcode[Tvar[j]][ij]=k; 
       fputs(line,ficparo);            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     }            
     ungetc(c,ficpar);            ij++;
            }
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);          if (ij > ncodemax[j]) break; 
            }  
     if (fage <= 2) {      } 
       bage = agemin;    }  
       fage = agemax;  
     }   for (k=0; k< maxncov; k++) Ndum[k]=0;
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");   for (i=1; i<=ncovmodel-2; i++) { 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);     ij=Tvar[i];
       Ndum[ij]++;
     while((c=getc(ficpar))=='#' && c!= EOF){   }
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);   ij=1;
     puts(line);   for (i=1; i<= maxncov; i++) {
     fputs(line,ficparo);     if((Ndum[i]!=0) && (i<=ncovcol)){
   }       Tvaraff[ij]=i; /*For printing */
   ungetc(c,ficpar);       ij++;
       }
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);   }
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);   
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);   cptcoveff=ij-1; /*Number of simple covariates*/
        }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  /*********** Health Expectancies ****************/
     fgets(line, MAXLINE, ficpar);  
     puts(line);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
     fputs(line,ficparo);  
   }  {
   ungetc(c,ficpar);    /* Health expectancies, no variances */
      int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
     int nhstepma, nstepma; /* Decreasing with age */
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    double age, agelim, hf;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    double ***p3mat;
     double eip;
   fscanf(ficpar,"pop_based=%d\n",&popbased);  
    fprintf(ficparo,"pop_based=%d\n",popbased);      pstamp(ficreseij);
    fprintf(ficres,"pop_based=%d\n",popbased);      fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     fprintf(ficreseij,"# Age");
   while((c=getc(ficpar))=='#' && c!= EOF){    for(i=1; i<=nlstate;i++){
     ungetc(c,ficpar);      for(j=1; j<=nlstate;j++){
     fgets(line, MAXLINE, ficpar);        fprintf(ficreseij," e%1d%1d ",i,j);
     puts(line);      }
     fputs(line,ficparo);      fprintf(ficreseij," e%1d. ",i);
   }    }
   ungetc(c,ficpar);    fprintf(ficreseij,"\n");
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);  
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);    }
     else  hstepm=estepm;   
        /* We compute the life expectancy from trapezoids spaced every estepm months
     /*------------ gnuplot -------------*/     * This is mainly to measure the difference between two models: for example
     /*chdir(pathcd);*/     * if stepm=24 months pijx are given only every 2 years and by summing them
     strcpy(optionfilegnuplot,optionfilefiname);     * we are calculating an estimate of the Life Expectancy assuming a linear 
     strcat(optionfilegnuplot,".plt");     * progression in between and thus overestimating or underestimating according
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {     * to the curvature of the survival function. If, for the same date, we 
       printf("Problem with file %s",optionfilegnuplot);goto end;     * 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 
 #ifdef windows     * hypothesis. A more precise result, taking into account a more precise
     fprintf(ficgp,"cd \"%s\" \n",pathc);     * curvature will be obtained if estepm is as small as stepm. */
 #endif  
 m=pow(2,cptcoveff);    /* For example we decided to compute the life expectancy with the smallest unit */
      /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
  /* 1eme*/       nhstepm is the number of hstepm from age to agelim 
   for (cpt=1; cpt<= nlstate ; cpt ++) {       nstepm is the number of stepm from age to agelin. 
    for (k1=1; k1<= m ; k1 ++) {       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
 #ifdef windows    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     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);       survival function given by stepm (the optimization length). Unfortunately it
 #endif       means that if the survival funtion is printed only each two years of age and if
 #ifdef unix       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);       results. So we changed our mind and took the option of the best precision.
 #endif    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    agelim=AGESUP;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /* If stepm=6 months */
 }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     for (i=1; i<= nlstate ; i ++) {      
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  /* nhstepm age range expressed in number of stepm */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
 }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    /* if (stepm >= YEARM) hstepm=1;*/
      for (i=1; i<= nlstate ; i ++) {    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      for (age=bage; age<=fage; age ++){ 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
 #ifdef unix      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 fprintf(ficgp,"\nset ter gif small size 400,300");      /* if (stepm >= YEARM) hstepm=1;*/
 #endif      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
    }      /* If stepm=6 months */
   }      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   /*2 eme*/         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
   for (k1=1; k1<= m ; k1 ++) {      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);      
          hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     for (i=1; i<= nlstate+1 ; i ++) {      
       k=2*i;      printf("%d|",(int)age);fflush(stdout);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       for (j=1; j<= nlstate+1 ; j ++) {      
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      /* Computing expectancies */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(i=1; i<=nlstate;i++)
 }          for(j=1; j<=nlstate;j++)
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);            
       for (j=1; j<= nlstate+1 ; j ++) {            /* if((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]);*/
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
         else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }    
       fprintf(ficgp,"\" t\"\" w l 0,");      fprintf(ficreseij,"%3.0f",age );
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      for(i=1; i<=nlstate;i++){
       for (j=1; j<= nlstate+1 ; j ++) {        eip=0;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(j=1; j<=nlstate;j++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          eip +=eij[i][j][(int)age];
 }            fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        }
       else fprintf(ficgp,"\" t\"\" w l 0,");        fprintf(ficreseij,"%9.4f", eip );
     }      }
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      fprintf(ficreseij,"\n");
   }      
      }
   /*3eme*/    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
   for (k1=1; k1<= m ; k1 ++) {    fprintf(ficlog,"\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {    
       k=2+nlstate*(cpt-1);  }
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);  
       for (i=1; i< nlstate ; i ++) {  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[] )
         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);  
       }  {
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    /* Covariances of health expectancies eij and of total life expectancies according
     }     to initial status i, ei. .
   }    */
      int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   /* CV preval stat */    int nhstepma, nstepma; /* Decreasing with age */
   for (k1=1; k1<= m ; k1 ++) {    double age, agelim, hf;
     for (cpt=1; cpt<nlstate ; cpt ++) {    double ***p3matp, ***p3matm, ***varhe;
       k=3;    double **dnewm,**doldm;
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);    double *xp, *xm;
       for (i=1; i< nlstate ; i ++)    double **gp, **gm;
         fprintf(ficgp,"+$%d",k+i+1);    double ***gradg, ***trgradg;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    int theta;
        
       l=3+(nlstate+ndeath)*cpt;    double eip, vip;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  
       for (i=1; i< nlstate ; i ++) {    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
         l=3+(nlstate+ndeath)*cpt;    xp=vector(1,npar);
         fprintf(ficgp,"+$%d",l+i+1);    xm=vector(1,npar);
       }    dnewm=matrix(1,nlstate*nlstate,1,npar);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    
     }    pstamp(ficresstdeij);
   }      fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
   /* proba elementaires */    for(i=1; i<=nlstate;i++){
    for(i=1,jk=1; i <=nlstate; i++){      for(j=1; j<=nlstate;j++)
     for(k=1; k <=(nlstate+ndeath); k++){        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       if (k != i) {      fprintf(ficresstdeij," e%1d. ",i);
         for(j=1; j <=ncovmodel; j++){    }
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/    fprintf(ficresstdeij,"\n");
           /*fprintf(ficgp,"%s",alph[1]);*/  
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    pstamp(ficrescveij);
           jk++;    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
           fprintf(ficgp,"\n");    fprintf(ficrescveij,"# Age");
         }    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++){
   for(jk=1; jk <=m; jk++) {            cptj2= (j2-1)*nlstate+i2;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);            if(cptj2 <= cptj)
    i=1;              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
    for(k2=1; k2<=nlstate; k2++) {          }
      k3=i;      }
      for(k=1; k<=(nlstate+ndeath); k++) {    fprintf(ficrescveij,"\n");
        if (k != k2){    
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    if(estepm < stepm){
 ij=1;      printf ("Problem %d lower than %d\n",estepm, stepm);
         for(j=3; j <=ncovmodel; j++) {    }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    else  hstepm=estepm;   
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    /* We compute the life expectancy from trapezoids spaced every estepm months
             ij++;     * This is mainly to measure the difference between two models: for example
           }     * if stepm=24 months pijx are given only every 2 years and by summing them
           else     * we are calculating an estimate of the Life Expectancy assuming a linear 
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);     * progression in between and thus overestimating or underestimating according
         }     * to the curvature of the survival function. If, for the same date, we 
           fprintf(ficgp,")/(1");     * 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 
         for(k1=1; k1 <=nlstate; k1++){       * hypothesis. A more precise result, taking into account a more precise
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);     * curvature will be obtained if estepm is as small as stepm. */
 ij=1;  
           for(j=3; j <=ncovmodel; j++){    /* For example we decided to compute the life expectancy with the smallest unit */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);       nhstepm is the number of hstepm from age to agelim 
             ij++;       nstepm is the number of stepm from age to agelin. 
           }       Look at hpijx to understand the reason of that which relies in memory size
           else       and note for a fixed period like estepm months */
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           }       survival function given by stepm (the optimization length). Unfortunately it
           fprintf(ficgp,")");       means that if the survival funtion is printed only each two years of age and if
         }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);       results. So we changed our mind and took the option of the best precision.
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    */
         i=i+ncovmodel;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
        }  
      }    /* If stepm=6 months */
    }    /* nhstepm age range expressed in number of stepm */
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    agelim=AGESUP;
   }    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
        /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   fclose(ficgp);    /* if (stepm >= YEARM) hstepm=1;*/
   /* end gnuplot */    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
        
 chdir(path);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ivector(wav,1,imx);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
     free_ivector(num,1,n);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
     free_vector(agedc,1,n);  
     /*free_matrix(covar,1,NCOVMAX,1,n);*/    for (age=bage; age<=fage; age ++){ 
     fclose(ficparo);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     fclose(ficres);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /*  }*/      /* if (stepm >= YEARM) hstepm=1;*/
          nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
    /*________fin mle=1_________*/  
          /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
           in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     /* No more information from the sample is required now */      
   /* Reads comments: lines beginning with '#' */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      /* Computing  Variances of health expectancies */
     fgets(line, MAXLINE, ficpar);      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
     puts(line);         decrease memory allocation */
     fputs(line,ficparo);      for(theta=1; theta <=npar; theta++){
   }        for(i=1; i<=npar; i++){ 
   ungetc(c,ficpar);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
            xm[i] = x[i] - (i==theta ?delti[theta]:0);
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);        }
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
 /*--------- index.htm --------*/    
         for(j=1; j<= nlstate; j++){
   strcpy(optionfilehtm,optionfile);          for(i=1; i<=nlstate; i++){
   strcat(optionfilehtm,".htm");            for(h=0; h<=nhstepm-1; h++){
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
     printf("Problem with %s \n",optionfilehtm);goto end;              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
   }            }
           }
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">        }
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>       
 Total number of observations=%d <br>        for(ij=1; ij<= nlstate*nlstate; ij++)
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>          for(h=0; h<=nhstepm-1; h++){
 <hr  size=\"2\" color=\"#EC5E5E\">            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
 <li>Outputs files<br><br>\n          }
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n      }/* End theta */
 - 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>      
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>      for(h=0; h<=nhstepm-1; h++)
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>        for(j=1; j<=nlstate*nlstate;j++)
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>          for(theta=1; theta <=npar; theta++)
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>            trgradg[h][j][theta]=gradg[h][theta][j];
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>      
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>  
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>       for(ij=1;ij<=nlstate*nlstate;ij++)
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);        for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
  fprintf(fichtm," <li>Graphs</li><p>");  
        printf("%d|",(int)age);fflush(stdout);
  m=cptcoveff;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
  j1=0;          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
  for(k1=1; k1<=m;k1++){          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
    for(i1=1; i1<=ncodemax[k1];i1++){          for(ij=1;ij<=nlstate*nlstate;ij++)
        j1++;            for(ji=1;ji<=nlstate*nlstate;ji++)
        if (cptcovn > 0) {              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
          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[j1][cpt]]);  
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      /* Computing expectancies */
        }      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      for(i=1; i<=nlstate;i++)
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            for(j=1; j<=nlstate;j++)
        for(cpt=1; cpt<nlstate;cpt++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);            
        }            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     for(cpt=1; cpt<=nlstate;cpt++) {  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          }
 interval) in state (%d): v%s%d%d.gif <br>  
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        fprintf(ficresstdeij,"%3.0f",age );
      }      for(i=1; i<=nlstate;i++){
      for(cpt=1; cpt<=nlstate;cpt++) {        eip=0.;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        vip=0.;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        for(j=1; j<=nlstate;j++){
      }          eip += eij[i][j][(int)age];
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
 health expectancies in states (1) and (2): e%s%d.gif<br>            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
 fprintf(fichtm,"\n</body>");        }
    }        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
  }      }
 fclose(fichtm);      fprintf(ficresstdeij,"\n");
   
   /*--------------- Prevalence limit --------------*/      fprintf(ficrescveij,"%3.0f",age );
        for(i=1; i<=nlstate;i++)
   strcpy(filerespl,"pl");        for(j=1; j<=nlstate;j++){
   strcat(filerespl,fileres);          cptj= (j-1)*nlstate+i;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          for(i2=1; i2<=nlstate;i2++)
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;            for(j2=1; j2<=nlstate;j2++){
   }              cptj2= (j2-1)*nlstate+i2;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);              if(cptj2 <= cptj)
   fprintf(ficrespl,"#Prevalence limit\n");                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
   fprintf(ficrespl,"#Age ");            }
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        }
   fprintf(ficrespl,"\n");      fprintf(ficrescveij,"\n");
       
   prlim=matrix(1,nlstate,1,nlstate);    }
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   k=0;    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   agebase=agemin;    printf("\n");
   agelim=agemax;    fprintf(ficlog,"\n");
   ftolpl=1.e-10;  
   i1=cptcoveff;    free_vector(xm,1,npar);
   if (cptcovn < 1){i1=1;}    free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   for(cptcov=1;cptcov<=i1;cptcov++){    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
         k=k+1;  }
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  
         fprintf(ficrespl,"\n#******");  /************ Variance ******************/
         for(j=1;j<=cptcoveff;j++)  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  {
         fprintf(ficrespl,"******\n");    /* Variance of health expectancies */
            /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
         for (age=agebase; age<=agelim; age++){    /* double **newm;*/
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    double **dnewm,**doldm;
           fprintf(ficrespl,"%.0f",age );    double **dnewmp,**doldmp;
           for(i=1; i<=nlstate;i++)    int i, j, nhstepm, hstepm, h, nstepm ;
           fprintf(ficrespl," %.5f", prlim[i][i]);    int k, cptcode;
           fprintf(ficrespl,"\n");    double *xp;
         }    double **gp, **gm;  /* for var eij */
       }    double ***gradg, ***trgradg; /*for var eij */
     }    double **gradgp, **trgradgp; /* for var p point j */
   fclose(ficrespl);    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   /*------------- h Pij x at various ages ------------*/    double ***p3mat;
      double age,agelim, hf;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    double ***mobaverage;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    int theta;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    char digit[4];
   }    char digitp[25];
   printf("Computing pij: result on file '%s' \n", filerespij);  
      char fileresprobmorprev[FILENAMELENGTH];
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   /*if (stepm<=24) stepsize=2;*/    if(popbased==1){
       if(mobilav!=0)
   agelim=AGESUP;        strcpy(digitp,"-populbased-mobilav-");
   hstepm=stepsize*YEARM; /* Every year of age */      else strcpy(digitp,"-populbased-nomobil-");
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    }
      else 
   k=0;      strcpy(digitp,"-stablbased-");
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    if (mobilav!=0) {
       k=k+1;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         fprintf(ficrespij,"\n#****** ");      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         for(j=1;j<=cptcoveff;j++)        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
         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 */    strcpy(fileresprobmorprev,"prmorprev"); 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    sprintf(digit,"%-d",ij);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
           oldm=oldms;savm=savms;    strcat(fileresprobmorprev,digit); /* Tvar to be done */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
           fprintf(ficrespij,"# Age");    strcat(fileresprobmorprev,fileres);
           for(i=1; i<=nlstate;i++)    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
             for(j=1; j<=nlstate+ndeath;j++)      printf("Problem with resultfile: %s\n", fileresprobmorprev);
               fprintf(ficrespij," %1d-%1d",i,j);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
           fprintf(ficrespij,"\n");    }
           for (h=0; h<=nhstepm; h++){    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );   
             for(i=1; i<=nlstate;i++)    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
               for(j=1; j<=nlstate+ndeath;j++)    pstamp(ficresprobmorprev);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    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(ficrespij,"\n");    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
           }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficresprobmorprev," p.%-d SE",j);
           fprintf(ficrespij,"\n");      for(i=1; i<=nlstate;i++)
         }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }    }  
   }    fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    /* 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");
   fclose(ficrespij);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
   if(stepm == 1) {    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   /*---------- Forecasting ------------------*/    pstamp(ficresvij);
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
   /*printf("calage= %f", calagedate);*/      fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
      else
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
   strcpy(fileresf,"f");      for(j=1; j<=nlstate;j++)
   strcat(fileresf,fileres);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    fprintf(ficresvij,"\n");
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;  
   }    xp=vector(1,npar);
   printf("Computing forecasting: result on file '%s' \n", fileresf);    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
   free_matrix(mint,1,maxwav,1,n);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   free_matrix(anint,1,maxwav,1,n);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   free_matrix(agev,1,maxwav,1,imx);  
   /* Mobile average */    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   if (mobilav==1) {    
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if(estepm < stepm){
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)      printf ("Problem %d lower than %d\n",estepm, stepm);
       for (i=1; i<=nlstate;i++)    }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    else  hstepm=estepm;   
           mobaverage[(int)agedeb][i][cptcod]=0.;    /* For example we decided to compute the life expectancy with the smallest unit */
        /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     for (agedeb=bage+4; agedeb<=fage; agedeb++){       nhstepm is the number of hstepm from age to agelim 
       for (i=1; i<=nlstate;i++){       nstepm is the number of stepm from age to agelin. 
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       Look at hpijx to understand the reason of that which relies in memory size
           for (cpt=0;cpt<=4;cpt++){       and note for a fixed period like k years */
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           }       survival function given by stepm (the optimization length). Unfortunately it
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;       means that if the survival funtion is printed every two years of age and if
         }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       }       results. So we changed our mind and took the option of the best precision.
     }      */
   }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   if (stepm<=12) stepsize=1;      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   agelim=AGESUP;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*hstepm=stepsize*YEARM; *//* Every year of age */      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   hstepm=1;      gp=matrix(0,nhstepm,1,nlstate);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */      gm=matrix(0,nhstepm,1,nlstate);
   yp1=modf(dateintmean,&yp);  
   anprojmean=yp;  
   yp2=modf((yp1*12),&yp);      for(theta=1; theta <=npar; theta++){
   mprojmean=yp;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   yp1=modf((yp2*30.5),&yp);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   jprojmean=yp;        }
   if(jprojmean==0) jprojmean=1;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   if(mprojmean==0) jprojmean=1;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        if (popbased==1) {
           if(mobilav ==0){
   if (popforecast==1) {            for(i=1; i<=nlstate;i++)
     if((ficpop=fopen(popfile,"r"))==NULL)    {              prlim[i][i]=probs[(int)age][i][ij];
       printf("Problem with population file : %s\n",popfile);goto end;          }else{ /* mobilav */ 
     }            for(i=1; i<=nlstate;i++)
     popage=ivector(0,AGESUP);              prlim[i][i]=mobaverage[(int)age][i][ij];
     popeffectif=vector(0,AGESUP);          }
     popcount=vector(0,AGESUP);        }
     
     i=1;          for(j=1; j<= nlstate; j++){
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)          for(h=0; h<=nhstepm; h++){
       {            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
         i=i+1;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
       }          }
     imx=i;        }
            /* This for computing probability of death (h=1 means
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];           computed over hstepm matrices product = hstepm*stepm months) 
   }           as a weighted average of prlim.
         */
   for(cptcov=1;cptcov<=i1;cptcov++){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          for(i=1,gpp[j]=0.; i<= nlstate; i++)
       k=k+1;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
       fprintf(ficresf,"\n#******");        }    
       for(j=1;j<=cptcoveff;j++) {        /* end probability of death */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
       fprintf(ficresf,"******\n");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       fprintf(ficresf,"# StartingAge FinalAge");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       if (popforecast==1)  fprintf(ficresf," [Population]");   
            if (popbased==1) {
       for (cpt=0; cpt<4;cpt++) {          if(mobilav ==0){
         fprintf(ficresf,"\n");            for(i=1; i<=nlstate;i++)
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);                prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */            for(i=1; i<=nlstate;i++)
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              prlim[i][i]=mobaverage[(int)age][i][ij];
         nhstepm = nhstepm/hstepm;          }
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/        }
   
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(j=1; j<= nlstate; j++){
         oldm=oldms;savm=savms;          for(h=0; h<=nhstepm; h++){
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                      gm[h][j] += prlim[i][i]*p3mat[i][j][h];
         for (h=0; h<=nhstepm; h++){          }
           if (h==(int) (calagedate+YEARM*cpt)) {        }
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);        /* This for computing probability of death (h=1 means
           }           computed over hstepm matrices product = hstepm*stepm months) 
           for(j=1; j<=nlstate+ndeath;j++) {           as a weighted average of prlim.
             kk1=0.;kk2=0;        */
             for(i=1; i<=nlstate;i++) {                for(j=nlstate+1;j<=nlstate+ndeath;j++){
               if (mobilav==1)          for(i=1,gmp[j]=0.; i<= nlstate; i++)
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];           gmp[j] += prlim[i][i]*p3mat[i][j][1];
               else {        }    
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        /* end probability of death */
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/  
               }        for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
             }          }
            
             if (h==(int)(calagedate+12*cpt)){        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
               fprintf(ficresf," %.3f", kk1);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
                      }
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);  
             }      } /* End theta */
           }  
         }      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
         /*      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);*/  
       }      for(h=0; h<=nhstepm; h++) /* veij */
       }        for(j=1; j<=nlstate;j++)
     }          for(theta=1; theta <=npar; theta++)
   }            trgradg[h][j][theta]=gradg[h][theta][j];
   /*  if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   if (popforecast==1) {      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     free_ivector(popage,0,AGESUP);        for(theta=1; theta <=npar; theta++)
     free_vector(popeffectif,0,AGESUP);          trgradgp[j][theta]=gradgp[theta][j];
     free_vector(popcount,0,AGESUP);    
   }  
   free_imatrix(s,1,maxwav+1,1,n);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   free_vector(weight,1,n);*/      for(i=1;i<=nlstate;i++)
   fclose(ficresf);        for(j=1;j<=nlstate;j++)
   }/* End forecasting */          vareij[i][j][(int)age] =0.;
   else{  
     erreur=108;      for(h=0;h<=nhstepm;h++){
     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);        for(k=0;k<=nhstepm;k++){
   }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   /*---------- Health expectancies and variances ------------*/          for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
   strcpy(filerest,"t");              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   strcat(filerest,fileres);        }
   if((ficrest=fopen(filerest,"w"))==NULL) {      }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    
   }      /* pptj */
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
   strcpy(filerese,"e");        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   strcat(filerese,fileres);          varppt[j][i]=doldmp[j][i];
   if((ficreseij=fopen(filerese,"w"))==NULL) {      /* end ppptj */
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      /*  x centered again */
   }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
  strcpy(fileresv,"v");      if (popbased==1) {
   strcat(fileresv,fileres);        if(mobilav ==0){
   if((ficresvij=fopen(fileresv,"w"))==NULL) {          for(i=1; i<=nlstate;i++)
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);            prlim[i][i]=probs[(int)age][i][ij];
   }        }else{ /* mobilav */ 
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
   k=0;        }
   for(cptcov=1;cptcov<=i1;cptcov++){      }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){               
       k=k+1;      /* This for computing probability of death (h=1 means
       fprintf(ficrest,"\n#****** ");         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       for(j=1;j<=cptcoveff;j++)         as a weighted average of prlim.
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      */
       fprintf(ficrest,"******\n");      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
       fprintf(ficreseij,"\n#****** ");          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       for(j=1;j<=cptcoveff;j++)      }    
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      /* end probability of death */
       fprintf(ficreseij,"******\n");  
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       fprintf(ficresvij,"\n#****** ");      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       for(j=1;j<=cptcoveff;j++)        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        for(i=1; i<=nlstate;i++){
       fprintf(ficresvij,"******\n");          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      } 
       oldm=oldms;savm=savms;      fprintf(ficresprobmorprev,"\n");
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);    
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      fprintf(ficresvij,"%.0f ",age );
       oldm=oldms;savm=savms;      for(i=1; i<=nlstate;i++)
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        for(j=1; j<=nlstate;j++){
                fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      fprintf(ficresvij,"\n");
       fprintf(ficrest,"\n");      free_matrix(gp,0,nhstepm,1,nlstate);
              free_matrix(gm,0,nhstepm,1,nlstate);
       hf=1;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       if (stepm >= YEARM) hf=stepm/YEARM;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       epj=vector(1,nlstate+1);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(age=bage; age <=fage ;age++){    } /* End age */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    free_vector(gpp,nlstate+1,nlstate+ndeath);
         if (popbased==1) {    free_vector(gmp,nlstate+1,nlstate+ndeath);
           for(i=1; i<=nlstate;i++)    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
             prlim[i][i]=probs[(int)age][i][k];    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         }    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
            /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
         fprintf(ficrest," %.0f",age);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
           for(i=1, epj[j]=0.;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); */
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
           }    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
           epj[nlstate+1] +=epj[j];    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
         }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
         for(i=1, vepp=0.;i <=nlstate;i++)    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
           for(j=1;j <=nlstate;j++)    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
             vepp += vareij[i][j][(int)age];    /*  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(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));  */
         for(j=1;j <=nlstate;j++){  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
         }  
         fprintf(ficrest,"\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);
            free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
  fclose(ficreseij);    fflush(ficgp);
  fclose(ficresvij);    fflush(fichtm); 
   fclose(ficrest);  }  /* end varevsij */
   fclose(ficpar);  
   free_vector(epj,1,nlstate+1);  /************ Variance of prevlim ******************/
   /*  scanf("%d ",i); */  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
   /*------- Variance limit prevalence------*/      /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
 strcpy(fileresvpl,"vpl");    double **newm;
   strcat(fileresvpl,fileres);    double **dnewm,**doldm;
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    int i, j, nhstepm, hstepm;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    int k, cptcode;
     exit(0);    double *xp;
   }    double *gp, *gm;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    double **gradg, **trgradg;
     double age,agelim;
  k=0;    int theta;
  for(cptcov=1;cptcov<=i1;cptcov++){    
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    pstamp(ficresvpl);
      k=k+1;    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
      fprintf(ficresvpl,"\n#****** ");    fprintf(ficresvpl,"# Age");
      for(j=1;j<=cptcoveff;j++)    for(i=1; i<=nlstate;i++)
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficresvpl," %1d-%1d",i,i);
      fprintf(ficresvpl,"******\n");    fprintf(ficresvpl,"\n");
        
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    xp=vector(1,npar);
      oldm=oldms;savm=savms;    dnewm=matrix(1,nlstate,1,npar);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    doldm=matrix(1,nlstate,1,nlstate);
    }    
  }    hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   fclose(ficresvpl);    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   /*---------- End : free ----------------*/      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      if (stepm >= YEARM) hstepm=1;
        nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      gradg=matrix(1,npar,1,nlstate);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      gp=vector(1,nlstate);
        gm=vector(1,nlstate);
    
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      for(theta=1; theta <=npar; theta++){
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        for(i=1; i<=npar; i++){ /* Computes gradient */
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        }
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   free_matrix(matcov,1,npar,1,npar);        for(i=1;i<=nlstate;i++)
   free_vector(delti,1,npar);          gp[i] = prlim[i][i];
        
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
   if(erreur >0)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     printf("End of Imach with error %d\n",erreur);        for(i=1;i<=nlstate;i++)
   else   printf("End of Imach\n");          gm[i] = prlim[i][i];
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
          for(i=1;i<=nlstate;i++)
   /* 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);*/          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   /*printf("Total time was %d uSec.\n", total_usecs);*/      } /* End theta */
   /*------ End -----------*/  
       trgradg =matrix(1,nlstate,1,npar);
   
  end:      for(j=1; j<=nlstate;j++)
 #ifdef windows        for(theta=1; theta <=npar; theta++)
   /* chdir(pathcd);*/          trgradg[j][theta]=gradg[theta][j];
 #endif  
  /*system("wgnuplot graph.plt");*/      for(i=1;i<=nlstate;i++)
  /*system("../gp37mgw/wgnuplot graph.plt");*/        varpl[i][(int)age] =0.;
  /*system("cd ../gp37mgw");*/      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
  strcpy(plotcmd,GNUPLOTPROGRAM);      for(i=1;i<=nlstate;i++)
  strcat(plotcmd," ");        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
  strcat(plotcmd,optionfilegnuplot);  
  system(plotcmd);      fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
 #ifdef windows        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   while (z[0] != 'q') {      fprintf(ficresvpl,"\n");
     chdir(path);      free_vector(gp,1,nlstate);
     printf("\nType e to edit output files, c to start again, and q for exiting: ");      free_vector(gm,1,nlstate);
     scanf("%s",z);      free_matrix(gradg,1,npar,1,nlstate);
     if (z[0] == 'c') system("./imach");      free_matrix(trgradg,1,nlstate,1,npar);
     else if (z[0] == 'e') {    } /* End age */
       chdir(path);  
       system(optionfilehtm);    free_vector(xp,1,npar);
     }    free_matrix(doldm,1,nlstate,1,npar);
     else if (z[0] == 'q') exit(0);    free_matrix(dnewm,1,nlstate,1,nlstate);
   }  
 #endif  }
 }  
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     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);
     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);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
    xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     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);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         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,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <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), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            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: <a href=\"%s\">%s</a> <br>\n",
            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): %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 m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char  *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       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++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
           exit(1);
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           exit(1);
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(1);
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(1);
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         exit(1);
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           exit(1);
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       } 
       lstra=strlen(stra);
       
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
     
       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;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* 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);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
           }
   
           pstamp(ficrest);
           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
     free_matrix(prlim,1,nlstate,1,nlstate);
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\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.1.24  
changed lines
  Added in v.1.127


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