Diff for /imach/src/imach.c between versions 1.41 and 1.129

version 1.41, 2002/05/07 15:53:01 version 1.129, 2007/08/31 13:49:27
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.129  2007/08/31 13:49:27  lievre
      Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.128  2006/06/30 13:02:05  brouard
   first survey ("cross") where individuals from different ages are    (Module): Clarifications on computing e.j
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.127  2006/04/28 18:11:50  brouard
   second wave of interviews ("longitudinal") which measure each change    (Module): Yes the sum of survivors was wrong since
   (if any) in individual health status.  Health expectancies are    imach-114 because nhstepm was no more computed in the age
   computed from the time spent in each health state according to a    loop. Now we define nhstepma in the age loop.
   model. More health states you consider, more time is necessary to reach the    (Module): In order to speed up (in case of numerous covariates) we
   Maximum Likelihood of the parameters involved in the model.  The    compute health expectancies (without variances) in a first step
   simplest model is the multinomial logistic model where pij is the    and then all the health expectancies with variances or standard
   probability to be observed in state j at the second wave    deviation (needs data from the Hessian matrices) which slows the
   conditional to be observed in state i at the first wave. Therefore    computation.
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    In the future we should be able to stop the program is only health
   'age' is age and 'sex' is a covariate. If you want to have a more    expectancies and graph are needed without standard deviations.
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.126  2006/04/28 17:23:28  brouard
   you to do it.  More covariates you add, slower the    (Module): Yes the sum of survivors was wrong since
   convergence.    imach-114 because nhstepm was no more computed in the age
     loop. Now we define nhstepma in the age loop.
   The advantage of this computer programme, compared to a simple    Version 0.98h
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.125  2006/04/04 15:20:31  lievre
   intermediate interview, the information is lost, but taken into    Errors in calculation of health expectancies. Age was not initialized.
   account using an interpolation or extrapolation.      Forecasting file added.
   
   hPijx is the probability to be observed in state i at age x+h    Revision 1.124  2006/03/22 17:13:53  lievre
   conditional to the observed state i at age x. The delay 'h' can be    Parameters are printed with %lf instead of %f (more numbers after the comma).
   split into an exact number (nh*stepm) of unobserved intermediate    The log-likelihood is printed in the log file
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.123  2006/03/20 10:52:43  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    * imach.c (Module): <title> changed, corresponds to .htm file
   and the contribution of each individual to the likelihood is simply    name. <head> headers where missing.
   hPijx.  
     * imach.c (Module): Weights can have a decimal point as for
   Also this programme outputs the covariance matrix of the parameters but also    English (a comma might work with a correct LC_NUMERIC environment,
   of the life expectancies. It also computes the prevalence limits.    otherwise the weight is truncated).
      Modification of warning when the covariates values are not 0 or
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    1.
            Institut national d'études démographiques, Paris.    Version 0.98g
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.122  2006/03/20 09:45:41  brouard
   It is copyrighted identically to a GNU software product, ie programme and    (Module): Weights can have a decimal point as for
   software can be distributed freely for non commercial use. Latest version    English (a comma might work with a correct LC_NUMERIC environment,
   can be accessed at http://euroreves.ined.fr/imach .    otherwise the weight is truncated).
   **********************************************************************/    Modification of warning when the covariates values are not 0 or
      1.
 #include <math.h>    Version 0.98g
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.121  2006/03/16 17:45:01  lievre
 #include <unistd.h>    * imach.c (Module): Comments concerning covariates added
   
 #define MAXLINE 256    * imach.c (Module): refinements in the computation of lli if
 #define GNUPLOTPROGRAM "wgnuplot"    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 1.120  2006/03/16 15:10:38  lievre
 #define windows    (Module): refinements in the computation of lli if
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    status=-2 in order to have more reliable computation if stepm is
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    not 1 month. Version 0.98f
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.119  2006/03/15 17:42:26  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Module): Bug if status = -2, the loglikelihood was
     computed as likelihood omitting the logarithm. Version O.98e
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.118  2006/03/14 18:20:07  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    (Module): varevsij Comments added explaining the second
 #define NCOVMAX 8 /* Maximum number of covariates */    table of variances if popbased=1 .
 #define MAXN 20000    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #define YEARM 12. /* Number of months per year */    (Module): Function pstamp added
 #define AGESUP 130    (Module): Version 0.98d
 #define AGEBASE 40  
     Revision 1.117  2006/03/14 17:16:22  brouard
     (Module): varevsij Comments added explaining the second
 int erreur; /* Error number */    table of variances if popbased=1 .
 int nvar;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    (Module): Function pstamp added
 int npar=NPARMAX;    (Module): Version 0.98d
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.116  2006/03/06 10:29:27  brouard
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    (Module): Variance-covariance wrong links and
 int popbased=0;    varian-covariance of ej. is needed (Saito).
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.115  2006/02/27 12:17:45  brouard
 int maxwav; /* Maxim number of waves */    (Module): One freematrix added in mlikeli! 0.98c
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.114  2006/02/26 12:57:58  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Module): Some improvements in processing parameter
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    filename with strsep.
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.113  2006/02/24 14:20:24  brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    (Module): Memory leaks checks with valgrind and:
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    datafile was not closed, some imatrix were not freed and on matrix
 FILE *ficgp,*ficresprob,*ficpop;    allocation too.
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.112  2006/01/30 09:55:26  brouard
  FILE  *ficresvij;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.111  2006/01/25 20:38:18  brouard
   char fileresvpl[FILENAMELENGTH];    (Module): Lots of cleaning and bugs added (Gompertz)
     (Module): Comments can be added in data file. Missing date values
 #define NR_END 1    can be a simple dot '.'.
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.110  2006/01/25 00:51:50  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 #define NRANSI  
 #define ITMAX 200    Revision 1.109  2006/01/24 19:37:15  brouard
     (Module): Comments (lines starting with a #) are allowed in data.
 #define TOL 2.0e-4  
     Revision 1.108  2006/01/19 18:05:42  lievre
 #define CGOLD 0.3819660    Gnuplot problem appeared...
 #define ZEPS 1.0e-10    To be fixed
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.107  2006/01/19 16:20:37  brouard
 #define GOLD 1.618034    Test existence of gnuplot in imach path
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.106  2006/01/19 13:24:36  brouard
     Some cleaning and links added in html output
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.105  2006/01/05 20:23:19  lievre
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    *** empty log message ***
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.104  2005/09/30 16:11:43  lievre
 #define rint(a) floor(a+0.5)    (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
 static double sqrarg;    that the person is alive, then we can code his/her status as -2
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    (instead of missing=-1 in earlier versions) and his/her
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    contributions to the likelihood is 1 - Prob of dying from last
     health status (= 1-p13= p11+p12 in the easiest case of somebody in
 int imx;    the healthy state at last known wave). Version is 0.98
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.103  2005/09/30 15:54:49  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
 int estepm;  
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    Revision 1.102  2004/09/15 17:31:30  brouard
     Add the possibility to read data file including tab characters.
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.101  2004/09/15 10:38:38  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Fix on curr_time
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;    Revision 1.100  2004/07/12 18:29:06  brouard
     Add version for Mac OS X. Just define UNIX in Makefile
 double *weight;  
 int **s; /* Status */    Revision 1.99  2004/06/05 08:57:40  brouard
 double *agedc, **covar, idx;    *** empty log message ***
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.98  2004/05/16 15:05:56  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    New version 0.97 . First attempt to estimate force of mortality
 double ftolhess; /* Tolerance for computing hessian */    directly from the data i.e. without the need of knowing the health
     state at each age, but using a Gompertz model: log u =a + b*age .
 /**************** split *************************/    This is the basic analysis of mortality and should be done before any
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    other analysis, in order to test if the mortality estimated from the
 {    cross-longitudinal survey is different from the mortality estimated
    char *s;                             /* pointer */    from other sources like vital statistic data.
    int  l1, l2;                         /* length counters */  
     The same imach parameter file can be used but the option for mle should be -3.
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Agnès, who wrote this part of the code, tried to keep most of the
 #ifdef windows    former routines in order to include the new code within the former code.
    s = strrchr( path, '\\' );           /* find last / */  
 #else    The output is very simple: only an estimate of the intercept and of
    s = strrchr( path, '/' );            /* find last / */    the slope with 95% confident intervals.
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */    Current limitations:
 #if     defined(__bsd__)                /* get current working directory */    A) Even if you enter covariates, i.e. with the
       extern char       *getwd( );    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
     B) There is no computation of Life Expectancy nor Life Table.
       if ( getwd( dirc ) == NULL ) {  
 #else    Revision 1.97  2004/02/20 13:25:42  lievre
       extern char       *getcwd( );    Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.96  2003/07/15 15:38:55  brouard
          return( GLOCK_ERROR_GETCWD );    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
       }    rewritten within the same printf. Workaround: many printfs.
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.95  2003/07/08 07:54:34  brouard
       s++;                              /* after this, the filename */    * imach.c (Repository):
       l2 = strlen( s );                 /* length of filename */    (Repository): Using imachwizard code to output a more meaningful covariance
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    matrix (cov(a12,c31) instead of numbers.
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Revision 1.94  2003/06/27 13:00:02  brouard
       dirc[l1-l2] = 0;                  /* add zero */    Just cleaning
    }  
    l1 = strlen( dirc );                 /* length of directory */    Revision 1.93  2003/06/25 16:33:55  brouard
 #ifdef windows    (Module): On windows (cygwin) function asctime_r doesn't
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    exist so I changed back to asctime which exists.
 #else    (Module): Version 0.96b
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif    Revision 1.92  2003/06/25 16:30:45  brouard
    s = strrchr( name, '.' );            /* find last / */    (Module): On windows (cygwin) function asctime_r doesn't
    s++;    exist so I changed back to asctime which exists.
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);    Revision 1.91  2003/06/25 15:30:29  brouard
    l2= strlen( s)+1;    * imach.c (Repository): Duplicated warning errors corrected.
    strncpy( finame, name, l1-l2);    (Repository): Elapsed time after each iteration is now output. It
    finame[l1-l2]= 0;    helps to forecast when convergence will be reached. Elapsed time
    return( 0 );                         /* we're done */    is stamped in powell.  We created a new html file for the graphs
 }    concerning matrix of covariance. It has extension -cov.htm.
   
     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
 void replace(char *s, char*t)    of the covariance matrix to be input.
 {  
   int i;    Revision 1.89  2003/06/24 12:30:52  brouard
   int lg=20;    (Module): Some bugs corrected for windows. Also, when
   i=0;    mle=-1 a template is output in file "or"mypar.txt with the design
   lg=strlen(t);    of the covariance matrix to be input.
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.88  2003/06/23 17:54:56  brouard
     if (t[i]== '\\') s[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.
   }  
 }    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
 int nbocc(char *s, char occ)  
 {    Revision 1.86  2003/06/17 20:04:08  brouard
   int i,j=0;    (Module): Change position of html and gnuplot routines and added
   int lg=20;    routine fileappend.
   i=0;  
   lg=strlen(s);    Revision 1.85  2003/06/17 13:12:43  brouard
   for(i=0; i<= lg; i++) {    * imach.c (Repository): Check when date of death was earlier that
   if  (s[i] == occ ) j++;    current date of interview. It may happen when the death was just
   }    prior to the death. In this case, dh was negative and likelihood
   return j;    was wrong (infinity). We still send an "Error" but patch by
 }    assuming that the date of death was just one stepm after the
     interview.
 void cutv(char *u,char *v, char*t, char occ)    (Repository): Because some people have very long ID (first column)
 {    we changed int to long in num[] and we added a new lvector for
   int i,lg,j,p=0;    memory allocation. But we also truncated to 8 characters (left
   i=0;    truncation)
   for(j=0; j<=strlen(t)-1; j++) {    (Repository): No more line truncation errors.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
   lg=strlen(t);    place. It differs from routine "prevalence" which may be called
   for(j=0; j<p; j++) {    many times. Probs is memory consuming and must be used with
     (u[j] = t[j]);    parcimony.
   }    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
      u[p]='\0';  
     Revision 1.83  2003/06/10 13:39:11  lievre
    for(j=0; j<= lg; j++) {    *** empty log message ***
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }    Revision 1.82  2003/06/05 15:57:20  brouard
 }    Add log in  imach.c and  fullversion number is now printed.
   
 /********************** nrerror ********************/  */
   /*
 void nrerror(char error_text[])     Interpolated Markov Chain
 {  
   fprintf(stderr,"ERREUR ...\n");    Short summary of the programme:
   fprintf(stderr,"%s\n",error_text);    
   exit(1);    This program computes Healthy Life Expectancies from
 }    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 /*********************** vector *******************/    first survey ("cross") where individuals from different ages are
 double *vector(int nl, int nh)    interviewed on their health status or degree of disability (in the
 {    case of a health survey which is our main interest) -2- at least a
   double *v;    second wave of interviews ("longitudinal") which measure each change
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    (if any) in individual health status.  Health expectancies are
   if (!v) nrerror("allocation failure in vector");    computed from the time spent in each health state according to a
   return v-nl+NR_END;    model. More health states you consider, more time is necessary to reach the
 }    Maximum Likelihood of the parameters involved in the model.  The
     simplest model is the multinomial logistic model where pij is the
 /************************ free vector ******************/    probability to be observed in state j at the second wave
 void free_vector(double*v, int nl, int nh)    conditional to be observed in state i at the first wave. Therefore
 {    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   free((FREE_ARG)(v+nl-NR_END));    '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
     where the markup *Covariates have to be included here again* invites
 /************************ivector *******************************/    you to do it.  More covariates you add, slower the
 int *ivector(long nl,long nh)    convergence.
 {  
   int *v;    The advantage of this computer programme, compared to a simple
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    multinomial logistic model, is clear when the delay between waves is not
   if (!v) nrerror("allocation failure in ivector");    identical for each individual. Also, if a individual missed an
   return v-nl+NR_END;    intermediate interview, the information is lost, but taken into
 }    account using an interpolation or extrapolation.  
   
 /******************free ivector **************************/    hPijx is the probability to be observed in state i at age x+h
 void free_ivector(int *v, long nl, long nh)    conditional to the observed state i at age x. The delay 'h' can be
 {    split into an exact number (nh*stepm) of unobserved intermediate
   free((FREE_ARG)(v+nl-NR_END));    states. This elementary transition (by month, quarter,
 }    semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
 /******************* imatrix *******************************/    and the contribution of each individual to the likelihood is simply
 int **imatrix(long nrl, long nrh, long ncl, long nch)    hPijx.
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {    Also this programme outputs the covariance matrix of the parameters but also
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    of the life expectancies. It also computes the period (stable) prevalence. 
   int **m;    
      Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   /* allocate pointers to rows */             Institut national d'études démographiques, Paris.
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    This software have been partly granted by Euro-REVES, a concerted action
   if (!m) nrerror("allocation failure 1 in matrix()");    from the European Union.
   m += NR_END;    It is copyrighted identically to a GNU software product, ie programme and
   m -= nrl;    software can be distributed freely for non commercial use. Latest version
      can be accessed at http://euroreves.ined.fr/imach .
    
   /* allocate rows and set pointers to them */    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    
   m[nrl] += NR_END;    **********************************************************************/
   m[nrl] -= ncl;  /*
      main
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    read parameterfile
      read datafile
   /* return pointer to array of pointers to rows */    concatwav
   return m;    freqsummary
 }    if (mle >= 1)
       mlikeli
 /****************** free_imatrix *************************/    print results files
 void free_imatrix(m,nrl,nrh,ncl,nch)    if mle==1 
       int **m;       computes hessian
       long nch,ncl,nrh,nrl;    read end of parameter file: agemin, agemax, bage, fage, estepm
      /* free an int matrix allocated by imatrix() */        begin-prev-date,...
 {    open gnuplot file
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    open html file
   free((FREE_ARG) (m+nrl-NR_END));    period (stable) prevalence
 }     for age prevalim()
     h Pij x
 /******************* matrix *******************************/    variance of p varprob
 double **matrix(long nrl, long nrh, long ncl, long nch)    forecasting if prevfcast==1 prevforecast call prevalence()
 {    health expectancies
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    Variance-covariance of DFLE
   double **m;    prevalence()
      movingaverage()
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    varevsij() 
   if (!m) nrerror("allocation failure 1 in matrix()");    if popbased==1 varevsij(,popbased)
   m += NR_END;    total life expectancies
   m -= nrl;    Variance of period (stable) prevalence
    end
   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;  
    
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #include <math.h>
   return m;  #include <stdio.h>
 }  #include <stdlib.h>
   #include <string.h>
 /*************************free matrix ************************/  #include <unistd.h>
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {  #include <limits.h>
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #include <sys/types.h>
   free((FREE_ARG)(m+nrl-NR_END));  #include <sys/stat.h>
 }  #include <errno.h>
   extern int errno;
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  /* #include <sys/time.h> */
 {  #include <time.h>
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  #include "timeval.h"
   double ***m;  
   /* #include <libintl.h> */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  /* #define _(String) gettext (String) */
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  #define MAXLINE 256
   m -= nrl;  
   #define GNUPLOTPROGRAM "gnuplot"
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define FILENAMELENGTH 132
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  #define NINTERVMAX 8
   m[nrl][ncl] -= nll;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   for (j=ncl+1; j<=nch; j++)  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
     m[nrl][j]=m[nrl][j-1]+nlay;  #define NCOVMAX 8 /* Maximum number of covariates */
    #define MAXN 20000
   for (i=nrl+1; i<=nrh; i++) {  #define YEARM 12. /* Number of months per year */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #define AGESUP 130
     for (j=ncl+1; j<=nch; j++)  #define AGEBASE 40
       m[i][j]=m[i][j-1]+nlay;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   }  #ifdef UNIX
   return m;  #define DIRSEPARATOR '/'
 }  #define CHARSEPARATOR "/"
   #define ODIRSEPARATOR '\\'
 /*************************free ma3x ************************/  #else
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #define DIRSEPARATOR '\\'
 {  #define CHARSEPARATOR "\\"
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  #define ODIRSEPARATOR '/'
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #endif
   free((FREE_ARG)(m+nrl-NR_END));  
 }  /* $Id$ */
   /* $State$ */
 /***************** f1dim *************************/  
 extern int ncom;  char version[]="Imach version 0.98i, June 2006, INED-EUROREVES-Institut de longevite ";
 extern double *pcom,*xicom;  char fullversion[]="$Revision$ $Date$"; 
 extern double (*nrfunc)(double []);  char strstart[80];
    char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 double f1dim(double x)  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 {  int nvar;
   int j;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   double f;  int npar=NPARMAX;
   double *xt;  int nlstate=2; /* Number of live states */
    int ndeath=1; /* Number of dead states */
   xt=vector(1,ncom);  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  int popbased=0;
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  int *wav; /* Number of waves for this individuual 0 is possible */
   return f;  int maxwav; /* Maxim number of waves */
 }  int jmin, jmax; /* min, max spacing between 2 waves */
   int ijmin, ijmax; /* Individuals having jmin and jmax */ 
 /*****************brent *************************/  int gipmx, gsw; /* Global variables on the number of contributions 
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)                     to the likelihood and the sum of weights (done by funcone)*/
 {  int mle, weightopt;
   int iter;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   double a,b,d,etemp;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   double fu,fv,fw,fx;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   double ftemp;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  double jmean; /* Mean space between 2 waves */
   double e=0.0;  double **oldm, **newm, **savm; /* Working pointers to matrices */
    double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   a=(ax < cx ? ax : cx);  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   b=(ax > cx ? ax : cx);  FILE *ficlog, *ficrespow;
   x=w=v=bx;  int globpr; /* Global variable for printing or not */
   fw=fv=fx=(*f)(x);  double fretone; /* Only one call to likelihood */
   for (iter=1;iter<=ITMAX;iter++) {  long ipmx; /* Number of contributions */
     xm=0.5*(a+b);  double sw; /* Sum of weights */
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  char filerespow[FILENAMELENGTH];
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
     printf(".");fflush(stdout);  FILE *ficresilk;
 #ifdef DEBUG  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     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 *ficresprobmorprev;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  FILE *fichtm, *fichtmcov; /* Html File */
 #endif  FILE *ficreseij;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  char filerese[FILENAMELENGTH];
       *xmin=x;  FILE *ficresstdeij;
       return fx;  char fileresstde[FILENAMELENGTH];
     }  FILE *ficrescveij;
     ftemp=fu;  char filerescve[FILENAMELENGTH];
     if (fabs(e) > tol1) {  FILE  *ficresvij;
       r=(x-w)*(fx-fv);  char fileresv[FILENAMELENGTH];
       q=(x-v)*(fx-fw);  FILE  *ficresvpl;
       p=(x-v)*q-(x-w)*r;  char fileresvpl[FILENAMELENGTH];
       q=2.0*(q-r);  char title[MAXLINE];
       if (q > 0.0) p = -p;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
       q=fabs(q);  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       etemp=e;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       e=d;  char command[FILENAMELENGTH];
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  int  outcmd=0;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
         d=p/q;  
         u=x+d;  char filelog[FILENAMELENGTH]; /* Log file */
         if (u-a < tol2 || b-u < tol2)  char filerest[FILENAMELENGTH];
           d=SIGN(tol1,xm-x);  char fileregp[FILENAMELENGTH];
       }  char popfile[FILENAMELENGTH];
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
     fu=(*f)(u);  struct timezone tzp;
     if (fu <= fx) {  extern int gettimeofday();
       if (u >= x) a=x; else b=x;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
       SHFT(v,w,x,u)  long time_value;
         SHFT(fv,fw,fx,fu)  extern long time();
         } else {  char strcurr[80], strfor[80];
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  char *endptr;
             v=w;  long lval;
             w=u;  double dval;
             fv=fw;  
             fw=fu;  #define NR_END 1
           } else if (fu <= fv || v == x || v == w) {  #define FREE_ARG char*
             v=u;  #define FTOL 1.0e-10
             fv=fu;  
           }  #define NRANSI 
         }  #define ITMAX 200 
   }  
   nrerror("Too many iterations in brent");  #define TOL 2.0e-4 
   *xmin=x;  
   return fx;  #define CGOLD 0.3819660 
 }  #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 /****************** mnbrak ***********************/  
   #define GOLD 1.618034 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #define GLIMIT 100.0 
             double (*func)(double))  #define TINY 1.0e-20 
 {  
   double ulim,u,r,q, dum;  static double maxarg1,maxarg2;
   double fu;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
    #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   *fa=(*func)(*ax);    
   *fb=(*func)(*bx);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   if (*fb > *fa) {  #define rint(a) floor(a+0.5)
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  static double sqrarg;
       }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   *cx=(*bx)+GOLD*(*bx-*ax);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   *fc=(*func)(*cx);  int agegomp= AGEGOMP;
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  int imx; 
     q=(*bx-*cx)*(*fb-*fa);  int stepm=1;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  /* Stepm, step in month: minimum step interpolation*/
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  
     ulim=(*bx)+GLIMIT*(*cx-*bx);  int estepm;
     if ((*bx-u)*(u-*cx) > 0.0) {  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       fu=(*func)(u);  
     } else if ((*cx-u)*(u-ulim) > 0.0) {  int m,nb;
       fu=(*func)(u);  long *num;
       if (fu < *fc) {  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
           SHFT(*fb,*fc,fu,(*func)(u))  double **pmmij, ***probs;
           }  double *ageexmed,*agecens;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  double dateintmean=0;
       u=ulim;  
       fu=(*func)(u);  double *weight;
     } else {  int **s; /* Status */
       u=(*cx)+GOLD*(*cx-*bx);  double *agedc, **covar, idx;
       fu=(*func)(u);  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
     }  double *lsurv, *lpop, *tpop;
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
       }  double ftolhess; /* Tolerance for computing hessian */
 }  
   /**************** split *************************/
 /*************** linmin ************************/  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
 int ncom;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
 double *pcom,*xicom;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
 double (*nrfunc)(double []);    */ 
      char  *ss;                            /* pointer */
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    int   l1, l2;                         /* length counters */
 {  
   double brent(double ax, double bx, double cx,    l1 = strlen(path );                   /* length of path */
                double (*f)(double), double tol, double *xmin);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   double f1dim(double x);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    if ( ss == NULL ) {                   /* no directory, so determine current directory */
               double *fc, double (*func)(double));      strcpy( name, path );               /* we got the fullname name because no directory */
   int j;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   double xx,xmin,bx,ax;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   double fx,fb,fa;      /* get current working directory */
        /*    extern  char* getcwd ( char *buf , int len);*/
   ncom=n;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   pcom=vector(1,n);        return( GLOCK_ERROR_GETCWD );
   xicom=vector(1,n);      }
   nrfunc=func;      /* got dirc from getcwd*/
   for (j=1;j<=n;j++) {      printf(" DIRC = %s \n",dirc);
     pcom[j]=p[j];    } else {                              /* strip direcotry from path */
     xicom[j]=xi[j];      ss++;                               /* after this, the filename */
   }      l2 = strlen( ss );                  /* length of filename */
   ax=0.0;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   xx=1.0;      strcpy( name, ss );         /* save file name */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      dirc[l1-l2] = 0;                    /* add zero */
 #ifdef DEBUG      printf(" DIRC2 = %s \n",dirc);
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    }
 #endif    /* We add a separator at the end of dirc if not exists */
   for (j=1;j<=n;j++) {    l1 = strlen( dirc );                  /* length of directory */
     xi[j] *= xmin;    if( dirc[l1-1] != DIRSEPARATOR ){
     p[j] += xi[j];      dirc[l1] =  DIRSEPARATOR;
   }      dirc[l1+1] = 0; 
   free_vector(xicom,1,n);      printf(" DIRC3 = %s \n",dirc);
   free_vector(pcom,1,n);    }
 }    ss = strrchr( name, '.' );            /* find last / */
     if (ss >0){
 /*************** powell ************************/      ss++;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      strcpy(ext,ss);                     /* save extension */
             double (*func)(double []))      l1= strlen( name);
 {      l2= strlen(ss)+1;
   void linmin(double p[], double xi[], int n, double *fret,      strncpy( finame, name, l1-l2);
               double (*func)(double []));      finame[l1-l2]= 0;
   int i,ibig,j;    }
   double del,t,*pt,*ptt,*xit;  
   double fp,fptt;    return( 0 );                          /* we're done */
   double *xits;  }
   pt=vector(1,n);  
   ptt=vector(1,n);  
   xit=vector(1,n);  /******************************************/
   xits=vector(1,n);  
   *fret=(*func)(p);  void replace_back_to_slash(char *s, char*t)
   for (j=1;j<=n;j++) pt[j]=p[j];  {
   for (*iter=1;;++(*iter)) {    int i;
     fp=(*fret);    int lg=0;
     ibig=0;    i=0;
     del=0.0;    lg=strlen(t);
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    for(i=0; i<= lg; i++) {
     for (i=1;i<=n;i++)      (s[i] = t[i]);
       printf(" %d %.12f",i, p[i]);      if (t[i]== '\\') s[i]='/';
     printf("\n");    }
     for (i=1;i<=n;i++) {  }
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  int nbocc(char *s, char occ)
 #ifdef DEBUG  {
       printf("fret=%lf \n",*fret);    int i,j=0;
 #endif    int lg=20;
       printf("%d",i);fflush(stdout);    i=0;
       linmin(p,xit,n,fret,func);    lg=strlen(s);
       if (fabs(fptt-(*fret)) > del) {    for(i=0; i<= lg; i++) {
         del=fabs(fptt-(*fret));    if  (s[i] == occ ) j++;
         ibig=i;    }
       }    return j;
 #ifdef DEBUG  }
       printf("%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {  void cutv(char *u,char *v, char*t, char occ)
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  {
         printf(" x(%d)=%.12e",j,xit[j]);    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       }       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       for(j=1;j<=n;j++)       gives u="abcedf" and v="ghi2j" */
         printf(" p=%.12e",p[j]);    int i,lg,j,p=0;
       printf("\n");    i=0;
 #endif    for(j=0; j<=strlen(t)-1; j++) {
     }      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    }
 #ifdef DEBUG  
       int k[2],l;    lg=strlen(t);
       k[0]=1;    for(j=0; j<p; j++) {
       k[1]=-1;      (u[j] = t[j]);
       printf("Max: %.12e",(*func)(p));    }
       for (j=1;j<=n;j++)       u[p]='\0';
         printf(" %.12e",p[j]);  
       printf("\n");     for(j=0; j<= lg; j++) {
       for(l=0;l<=1;l++) {      if (j>=(p+1))(v[j-p-1] = t[j]);
         for (j=1;j<=n;j++) {    }
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  }
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  
         }  /********************** nrerror ********************/
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  void nrerror(char error_text[])
 #endif  {
     fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
       free_vector(xit,1,n);    exit(EXIT_FAILURE);
       free_vector(xits,1,n);  }
       free_vector(ptt,1,n);  /*********************** vector *******************/
       free_vector(pt,1,n);  double *vector(int nl, int nh)
       return;  {
     }    double *v;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     for (j=1;j<=n;j++) {    if (!v) nrerror("allocation failure in vector");
       ptt[j]=2.0*p[j]-pt[j];    return v-nl+NR_END;
       xit[j]=p[j]-pt[j];  }
       pt[j]=p[j];  
     }  /************************ free vector ******************/
     fptt=(*func)(ptt);  void free_vector(double*v, int nl, int nh)
     if (fptt < fp) {  {
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    free((FREE_ARG)(v+nl-NR_END));
       if (t < 0.0) {  }
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {  /************************ivector *******************************/
           xi[j][ibig]=xi[j][n];  int *ivector(long nl,long nh)
           xi[j][n]=xit[j];  {
         }    int *v;
 #ifdef DEBUG    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    if (!v) nrerror("allocation failure in ivector");
         for(j=1;j<=n;j++)    return v-nl+NR_END;
           printf(" %.12e",xit[j]);  }
         printf("\n");  
 #endif  /******************free ivector **************************/
       }  void free_ivector(int *v, long nl, long nh)
     }  {
   }    free((FREE_ARG)(v+nl-NR_END));
 }  }
   
 /**** Prevalence limit ****************/  /************************lvector *******************************/
   long *lvector(long nl,long nh)
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  {
 {    long *v;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
      matrix by transitions matrix until convergence is reached */    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
   int i, ii,j,k;  }
   double min, max, maxmin, maxmax,sumnew=0.;  
   double **matprod2();  /******************free lvector **************************/
   double **out, cov[NCOVMAX], **pmij();  void free_lvector(long *v, long nl, long nh)
   double **newm;  {
   double agefin, delaymax=50 ; /* Max number of years to converge */    free((FREE_ARG)(v+nl-NR_END));
   }
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){  /******************* imatrix *******************************/
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     }       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   { 
    cov[1]=1.;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
      int **m; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    /* allocate pointers to rows */ 
     newm=savm;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     /* Covariates have to be included here again */    if (!m) nrerror("allocation failure 1 in matrix()"); 
      cov[2]=agefin;    m += NR_END; 
      m -= nrl; 
       for (k=1; k<=cptcovn;k++) {    
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/    /* allocate rows and set pointers to them */ 
       }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       for (k=1; k<=cptcovprod;k++)    m[nrl] += NR_END; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    m[nrl] -= ncl; 
     
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    /* return pointer to array of pointers to rows */ 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    return m; 
   } 
     savm=oldm;  
     oldm=newm;  /****************** free_imatrix *************************/
     maxmax=0.;  void free_imatrix(m,nrl,nrh,ncl,nch)
     for(j=1;j<=nlstate;j++){        int **m;
       min=1.;        long nch,ncl,nrh,nrl; 
       max=0.;       /* free an int matrix allocated by imatrix() */ 
       for(i=1; i<=nlstate; i++) {  { 
         sumnew=0;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    free((FREE_ARG) (m+nrl-NR_END)); 
         prlim[i][j]= newm[i][j]/(1-sumnew);  } 
         max=FMAX(max,prlim[i][j]);  
         min=FMIN(min,prlim[i][j]);  /******************* matrix *******************************/
       }  double **matrix(long nrl, long nrh, long ncl, long nch)
       maxmin=max-min;  {
       maxmax=FMAX(maxmax,maxmin);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     }    double **m;
     if(maxmax < ftolpl){  
       return prlim;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     }    if (!m) nrerror("allocation failure 1 in matrix()");
   }    m += NR_END;
 }    m -= nrl;
   
 /*************** transition probabilities ***************/    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    m[nrl] += NR_END;
 {    m[nrl] -= ncl;
   double s1, s2;  
   /*double t34;*/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   int i,j,j1, nc, ii, jj;    return m;
     /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     for(i=1; i<= nlstate; i++){     */
     for(j=1; j<i;j++){  }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         /*s2 += param[i][j][nc]*cov[nc];*/  /*************************free matrix ************************/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  {
       }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       ps[i][j]=s2;    free((FREE_ARG)(m+nrl-NR_END));
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  }
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){  /******************* ma3x *******************************/
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
         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);*/    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       }    double ***m;
       ps[i][j]=s2;  
     }    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   }    if (!m) nrerror("allocation failure 1 in matrix()");
     /*ps[3][2]=1;*/    m += NR_END;
     m -= nrl;
   for(i=1; i<= nlstate; i++){  
      s1=0;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     for(j=1; j<i; j++)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       s1+=exp(ps[i][j]);    m[nrl] += NR_END;
     for(j=i+1; j<=nlstate+ndeath; j++)    m[nrl] -= ncl;
       s1+=exp(ps[i][j]);  
     ps[i][i]=1./(s1+1.);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     for(j=i+1; j<=nlstate+ndeath; j++)    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       ps[i][j]= exp(ps[i][j])*ps[i][i];    m[nrl][ncl] += NR_END;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    m[nrl][ncl] -= nll;
   } /* end i */    for (j=ncl+1; j<=nch; j++) 
       m[nrl][j]=m[nrl][j-1]+nlay;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    
     for(jj=1; jj<= nlstate+ndeath; jj++){    for (i=nrl+1; i<=nrh; i++) {
       ps[ii][jj]=0;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       ps[ii][ii]=1;      for (j=ncl+1; j<=nch; j++) 
     }        m[i][j]=m[i][j-1]+nlay;
   }    }
     return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     for(jj=1; jj<= nlstate+ndeath; jj++){    */
      printf("%lf ",ps[ii][jj]);  }
    }  
     printf("\n ");  /*************************free ma3x ************************/
     }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     printf("\n ");printf("%lf ",cov[2]);*/  {
 /*    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   goto end;*/    free((FREE_ARG)(m+nrl-NR_END));
     return ps;  }
 }  
   /*************** function subdirf ***********/
 /**************** Product of 2 matrices ******************/  char *subdirf(char fileres[])
   {
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    /* Caution optionfilefiname is hidden */
 {    strcpy(tmpout,optionfilefiname);
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    strcat(tmpout,"/"); /* Add to the right */
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    strcat(tmpout,fileres);
   /* in, b, out are matrice of pointers which should have been initialized    return tmpout;
      before: only the contents of out is modified. The function returns  }
      a pointer to pointers identical to out */  
   long i, j, k;  /*************** function subdirf2 ***********/
   for(i=nrl; i<= nrh; i++)  char *subdirf2(char fileres[], char *preop)
     for(k=ncolol; k<=ncoloh; k++)  {
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    
         out[i][k] +=in[i][j]*b[j][k];    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
   return out;    strcat(tmpout,"/");
 }    strcat(tmpout,preop);
     strcat(tmpout,fileres);
     return tmpout;
 /************* Higher Matrix Product ***************/  }
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  /*************** function subdirf3 ***********/
 {  char *subdirf3(char fileres[], char *preop, char *preop2)
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  {
      duration (i.e. until    
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    /* Caution optionfilefiname is hidden */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    strcpy(tmpout,optionfilefiname);
      (typically every 2 years instead of every month which is too big).    strcat(tmpout,"/");
      Model is determined by parameters x and covariates have to be    strcat(tmpout,preop);
      included manually here.    strcat(tmpout,preop2);
     strcat(tmpout,fileres);
      */    return tmpout;
   }
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];  /***************** f1dim *************************/
   double **newm;  extern int ncom; 
   extern double *pcom,*xicom;
   /* Hstepm could be zero and should return the unit matrix */  extern double (*nrfunc)(double []); 
   for (i=1;i<=nlstate+ndeath;i++)   
     for (j=1;j<=nlstate+ndeath;j++){  double f1dim(double x) 
       oldm[i][j]=(i==j ? 1.0 : 0.0);  { 
       po[i][j][0]=(i==j ? 1.0 : 0.0);    int j; 
     }    double f;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    double *xt; 
   for(h=1; h <=nhstepm; h++){   
     for(d=1; d <=hstepm; d++){    xt=vector(1,ncom); 
       newm=savm;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       /* Covariates have to be included here again */    f=(*nrfunc)(xt); 
       cov[1]=1.;    free_vector(xt,1,ncom); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    return f; 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  } 
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /*****************brent *************************/
       for (k=1; k<=cptcovprod;k++)  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  { 
     int iter; 
     double a,b,d,etemp;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    double fu,fv,fw,fx;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    double ftemp;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    double p,q,r,tol1,tol2,u,v,w,x,xm; 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    double e=0.0; 
       savm=oldm;   
       oldm=newm;    a=(ax < cx ? ax : cx); 
     }    b=(ax > cx ? ax : cx); 
     for(i=1; i<=nlstate+ndeath; i++)    x=w=v=bx; 
       for(j=1;j<=nlstate+ndeath;j++) {    fw=fv=fx=(*f)(x); 
         po[i][j][h]=newm[i][j];    for (iter=1;iter<=ITMAX;iter++) { 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      xm=0.5*(a+b); 
          */      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   } /* end h */      printf(".");fflush(stdout);
   return po;      fprintf(ficlog,".");fflush(ficlog);
 }  #ifdef DEBUG
       printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 /*************** log-likelihood *************/      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 double func( double *x)  #endif
 {      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   int i, ii, j, k, mi, d, kk;        *xmin=x; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        return fx; 
   double **out;      } 
   double sw; /* Sum of weights */      ftemp=fu;
   double lli; /* Individual log likelihood */      if (fabs(e) > tol1) { 
   long ipmx;        r=(x-w)*(fx-fv); 
   /*extern weight */        q=(x-v)*(fx-fw); 
   /* We are differentiating ll according to initial status */        p=(x-v)*q-(x-w)*r; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        q=2.0*(q-r); 
   /*for(i=1;i<imx;i++)        if (q > 0.0) p = -p; 
     printf(" %d\n",s[4][i]);        q=fabs(q); 
   */        etemp=e; 
   cov[1]=1.;        e=d; 
         if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   for(k=1; k<=nlstate; k++) ll[k]=0.;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        else { 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];          d=p/q; 
     for(mi=1; mi<= wav[i]-1; mi++){          u=x+d; 
       for (ii=1;ii<=nlstate+ndeath;ii++)          if (u-a < tol2 || b-u < tol2) 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);            d=SIGN(tol1,xm-x); 
       for(d=0; d<dh[mi][i]; d++){        } 
         newm=savm;      } else { 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         for (kk=1; kk<=cptcovage;kk++) {      } 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         }      fu=(*f)(u); 
              if (fu <= fx) { 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        if (u >= x) a=x; else b=x; 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        SHFT(v,w,x,u) 
         savm=oldm;          SHFT(fv,fw,fx,fu) 
         oldm=newm;          } else { 
                    if (u < x) a=u; else b=u; 
                    if (fu <= fw || w == x) { 
       } /* end mult */              v=w; 
                    w=u; 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);              fv=fw; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/              fw=fu; 
       ipmx +=1;            } else if (fu <= fv || v == x || v == w) { 
       sw += weight[i];              v=u; 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;              fv=fu; 
     } /* end of wave */            } 
   } /* end of individual */          } 
     } 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    nrerror("Too many iterations in brent"); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    *xmin=x; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    return fx; 
   return -l;  } 
 }  
   /****************** mnbrak ***********************/
   
 /*********** Maximum Likelihood Estimation ***************/  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               double (*func)(double)) 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  { 
 {    double ulim,u,r,q, dum;
   int i,j, iter;    double fu; 
   double **xi,*delti;   
   double fret;    *fa=(*func)(*ax); 
   xi=matrix(1,npar,1,npar);    *fb=(*func)(*bx); 
   for (i=1;i<=npar;i++)    if (*fb > *fa) { 
     for (j=1;j<=npar;j++)      SHFT(dum,*ax,*bx,dum) 
       xi[i][j]=(i==j ? 1.0 : 0.0);        SHFT(dum,*fb,*fa,dum) 
   printf("Powell\n");        } 
   powell(p,xi,npar,ftol,&iter,&fret,func);    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    while (*fb > *fc) { 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
 }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 /**** Computes Hessian and covariance matrix ***/      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      if ((*bx-u)*(u-*cx) > 0.0) { 
 {        fu=(*func)(u); 
   double  **a,**y,*x,pd;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   double **hess;        fu=(*func)(u); 
   int i, j,jk;        if (fu < *fc) { 
   int *indx;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
   double hessii(double p[], double delta, int theta, double delti[]);            } 
   double hessij(double p[], double delti[], int i, int j);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   void lubksb(double **a, int npar, int *indx, double b[]) ;        u=ulim; 
   void ludcmp(double **a, int npar, int *indx, double *d) ;        fu=(*func)(u); 
       } else { 
   hess=matrix(1,npar,1,npar);        u=(*cx)+GOLD*(*cx-*bx); 
         fu=(*func)(u); 
   printf("\nCalculation of the hessian matrix. Wait...\n");      } 
   for (i=1;i<=npar;i++){      SHFT(*ax,*bx,*cx,u) 
     printf("%d",i);fflush(stdout);        SHFT(*fa,*fb,*fc,fu) 
     hess[i][i]=hessii(p,ftolhess,i,delti);        } 
     /*printf(" %f ",p[i]);*/  } 
     /*printf(" %lf ",hess[i][i]);*/  
   }  /*************** linmin ************************/
    
   for (i=1;i<=npar;i++) {  int ncom; 
     for (j=1;j<=npar;j++)  {  double *pcom,*xicom;
       if (j>i) {  double (*nrfunc)(double []); 
         printf(".%d%d",i,j);fflush(stdout);   
         hess[i][j]=hessij(p,delti,i,j);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         hess[j][i]=hess[i][j];      { 
         /*printf(" %lf ",hess[i][j]);*/    double brent(double ax, double bx, double cx, 
       }                 double (*f)(double), double tol, double *xmin); 
     }    double f1dim(double x); 
   }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   printf("\n");                double *fc, double (*func)(double)); 
     int j; 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    double xx,xmin,bx,ax; 
      double fx,fb,fa;
   a=matrix(1,npar,1,npar);   
   y=matrix(1,npar,1,npar);    ncom=n; 
   x=vector(1,npar);    pcom=vector(1,n); 
   indx=ivector(1,npar);    xicom=vector(1,n); 
   for (i=1;i<=npar;i++)    nrfunc=func; 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    for (j=1;j<=n;j++) { 
   ludcmp(a,npar,indx,&pd);      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
   for (j=1;j<=npar;j++) {    } 
     for (i=1;i<=npar;i++) x[i]=0;    ax=0.0; 
     x[j]=1;    xx=1.0; 
     lubksb(a,npar,indx,x);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     for (i=1;i<=npar;i++){    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       matcov[i][j]=x[i];  #ifdef DEBUG
     }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   #endif
   printf("\n#Hessian matrix#\n");    for (j=1;j<=n;j++) { 
   for (i=1;i<=npar;i++) {      xi[j] *= xmin; 
     for (j=1;j<=npar;j++) {      p[j] += xi[j]; 
       printf("%.3e ",hess[i][j]);    } 
     }    free_vector(xicom,1,n); 
     printf("\n");    free_vector(pcom,1,n); 
   }  } 
   
   /* Recompute Inverse */  char *asc_diff_time(long time_sec, char ascdiff[])
   for (i=1;i<=npar;i++)  {
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    long sec_left, days, hours, minutes;
   ludcmp(a,npar,indx,&pd);    days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
   /*  printf("\n#Hessian matrix recomputed#\n");    hours = (sec_left) / (60*60) ;
     sec_left = (sec_left) %(60*60);
   for (j=1;j<=npar;j++) {    minutes = (sec_left) /60;
     for (i=1;i<=npar;i++) x[i]=0;    sec_left = (sec_left) % (60);
     x[j]=1;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     lubksb(a,npar,indx,x);    return ascdiff;
     for (i=1;i<=npar;i++){  }
       y[i][j]=x[i];  
       printf("%.3e ",y[i][j]);  /*************** powell ************************/
     }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     printf("\n");              double (*func)(double [])) 
   }  { 
   */    void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
   free_matrix(a,1,npar,1,npar);    int i,ibig,j; 
   free_matrix(y,1,npar,1,npar);    double del,t,*pt,*ptt,*xit;
   free_vector(x,1,npar);    double fp,fptt;
   free_ivector(indx,1,npar);    double *xits;
   free_matrix(hess,1,npar,1,npar);    int niterf, itmp;
   
     pt=vector(1,n); 
 }    ptt=vector(1,n); 
     xit=vector(1,n); 
 /*************** hessian matrix ****************/    xits=vector(1,n); 
 double hessii( double x[], double delta, int theta, double delti[])    *fret=(*func)(p); 
 {    for (j=1;j<=n;j++) pt[j]=p[j]; 
   int i;    for (*iter=1;;++(*iter)) { 
   int l=1, lmax=20;      fp=(*fret); 
   double k1,k2;      ibig=0; 
   double p2[NPARMAX+1];      del=0.0; 
   double res;      last_time=curr_time;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      (void) gettimeofday(&curr_time,&tzp);
   double fx;      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);
   int k=0,kmax=10;      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 l1;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
      for (i=1;i<=n;i++) {
   fx=func(x);        printf(" %d %.12f",i, p[i]);
   for (i=1;i<=npar;i++) p2[i]=x[i];        fprintf(ficlog," %d %.12lf",i, p[i]);
   for(l=0 ; l <=lmax; l++){        fprintf(ficrespow," %.12lf", p[i]);
     l1=pow(10,l);      }
     delts=delt;      printf("\n");
     for(k=1 ; k <kmax; k=k+1){      fprintf(ficlog,"\n");
       delt = delta*(l1*k);      fprintf(ficrespow,"\n");fflush(ficrespow);
       p2[theta]=x[theta] +delt;      if(*iter <=3){
       k1=func(p2)-fx;        tm = *localtime(&curr_time.tv_sec);
       p2[theta]=x[theta]-delt;        strcpy(strcurr,asctime(&tm));
       k2=func(p2)-fx;  /*       asctime_r(&tm,strcurr); */
       /*res= (k1-2.0*fx+k2)/delt/delt; */        forecast_time=curr_time; 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        itmp = strlen(strcurr);
              if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
 #ifdef DEBUG          strcurr[itmp-1]='\0';
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
 #endif        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        for(niterf=10;niterf<=30;niterf+=10){
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
         k=kmax;          tmf = *localtime(&forecast_time.tv_sec);
       }  /*      asctime_r(&tmf,strfor); */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          strcpy(strfor,asctime(&tmf));
         k=kmax; l=lmax*10.;          itmp = strlen(strfor);
       }          if(strfor[itmp-1]=='\n')
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          strfor[itmp-1]='\0';
         delts=delt;          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);
     }        }
   }      }
   delti[theta]=delts;      for (i=1;i<=n;i++) { 
   return res;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
          fptt=(*fret); 
 }  #ifdef DEBUG
         printf("fret=%lf \n",*fret);
 double hessij( double x[], double delti[], int thetai,int thetaj)        fprintf(ficlog,"fret=%lf \n",*fret);
 {  #endif
   int i;        printf("%d",i);fflush(stdout);
   int l=1, l1, lmax=20;        fprintf(ficlog,"%d",i);fflush(ficlog);
   double k1,k2,k3,k4,res,fx;        linmin(p,xit,n,fret,func); 
   double p2[NPARMAX+1];        if (fabs(fptt-(*fret)) > del) { 
   int k;          del=fabs(fptt-(*fret)); 
           ibig=i; 
   fx=func(x);        } 
   for (k=1; k<=2; k++) {  #ifdef DEBUG
     for (i=1;i<=npar;i++) p2[i]=x[i];        printf("%d %.12e",i,(*fret));
     p2[thetai]=x[thetai]+delti[thetai]/k;        fprintf(ficlog,"%d %.12e",i,(*fret));
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        for (j=1;j<=n;j++) {
     k1=func(p2)-fx;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
            printf(" x(%d)=%.12e",j,xit[j]);
     p2[thetai]=x[thetai]+delti[thetai]/k;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        }
     k2=func(p2)-fx;        for(j=1;j<=n;j++) {
            printf(" p=%.12e",p[j]);
     p2[thetai]=x[thetai]-delti[thetai]/k;          fprintf(ficlog," p=%.12e",p[j]);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        }
     k3=func(p2)-fx;        printf("\n");
          fprintf(ficlog,"\n");
     p2[thetai]=x[thetai]-delti[thetai]/k;  #endif
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      } 
     k4=func(p2)-fx;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  #ifdef DEBUG
 #ifdef DEBUG        int k[2],l;
     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);        k[0]=1;
 #endif        k[1]=-1;
   }        printf("Max: %.12e",(*func)(p));
   return res;        fprintf(ficlog,"Max: %.12e",(*func)(p));
 }        for (j=1;j<=n;j++) {
           printf(" %.12e",p[j]);
 /************** Inverse of matrix **************/          fprintf(ficlog," %.12e",p[j]);
 void ludcmp(double **a, int n, int *indx, double *d)        }
 {        printf("\n");
   int i,imax,j,k;        fprintf(ficlog,"\n");
   double big,dum,sum,temp;        for(l=0;l<=1;l++) {
   double *vv;          for (j=1;j<=n;j++) {
              ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   vv=vector(1,n);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   *d=1.0;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   for (i=1;i<=n;i++) {          }
     big=0.0;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for (j=1;j<=n;j++)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       if ((temp=fabs(a[i][j])) > big) big=temp;        }
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  #endif
     vv[i]=1.0/big;  
   }  
   for (j=1;j<=n;j++) {        free_vector(xit,1,n); 
     for (i=1;i<j;i++) {        free_vector(xits,1,n); 
       sum=a[i][j];        free_vector(ptt,1,n); 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        free_vector(pt,1,n); 
       a[i][j]=sum;        return; 
     }      } 
     big=0.0;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     for (i=j;i<=n;i++) {      for (j=1;j<=n;j++) { 
       sum=a[i][j];        ptt[j]=2.0*p[j]-pt[j]; 
       for (k=1;k<j;k++)        xit[j]=p[j]-pt[j]; 
         sum -= a[i][k]*a[k][j];        pt[j]=p[j]; 
       a[i][j]=sum;      } 
       if ( (dum=vv[i]*fabs(sum)) >= big) {      fptt=(*func)(ptt); 
         big=dum;      if (fptt < fp) { 
         imax=i;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       }        if (t < 0.0) { 
     }          linmin(p,xit,n,fret,func); 
     if (j != imax) {          for (j=1;j<=n;j++) { 
       for (k=1;k<=n;k++) {            xi[j][ibig]=xi[j][n]; 
         dum=a[imax][k];            xi[j][n]=xit[j]; 
         a[imax][k]=a[j][k];          }
         a[j][k]=dum;  #ifdef DEBUG
       }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       *d = -(*d);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       vv[imax]=vv[j];          for(j=1;j<=n;j++){
     }            printf(" %.12e",xit[j]);
     indx[j]=imax;            fprintf(ficlog," %.12e",xit[j]);
     if (a[j][j] == 0.0) a[j][j]=TINY;          }
     if (j != n) {          printf("\n");
       dum=1.0/(a[j][j]);          fprintf(ficlog,"\n");
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  #endif
     }        }
   }      } 
   free_vector(vv,1,n);  /* Doesn't work */    } 
 ;  } 
 }  
   /**** Prevalence limit (stable or period prevalence)  ****************/
 void lubksb(double **a, int n, int *indx, double b[])  
 {  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   int i,ii=0,ip,j;  {
   double sum;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         matrix by transitions matrix until convergence is reached */
   for (i=1;i<=n;i++) {  
     ip=indx[i];    int i, ii,j,k;
     sum=b[ip];    double min, max, maxmin, maxmax,sumnew=0.;
     b[ip]=b[i];    double **matprod2();
     if (ii)    double **out, cov[NCOVMAX], **pmij();
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    double **newm;
     else if (sum) ii=i;    double agefin, delaymax=50 ; /* Max number of years to converge */
     b[i]=sum;  
   }    for (ii=1;ii<=nlstate+ndeath;ii++)
   for (i=n;i>=1;i--) {      for (j=1;j<=nlstate+ndeath;j++){
     sum=b[i];        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      }
     b[i]=sum/a[i][i];  
   }     cov[1]=1.;
 }   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 /************ Frequencies ********************/    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)      newm=savm;
 {  /* Some frequencies */      /* Covariates have to be included here again */
         cov[2]=agefin;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    
   double ***freq; /* Frequencies */        for (k=1; k<=cptcovn;k++) {
   double *pp;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double pos, k2, dateintsum=0,k2cpt=0;          /*      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]]);*/
   FILE *ficresp;        }
   char fileresp[FILENAMELENGTH];        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
          for (k=1; k<=cptcovprod;k++)
   pp=vector(1,nlstate);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   strcpy(fileresp,"p");        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   strcat(fileresp,fileres);        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   if((ficresp=fopen(fileresp,"w"))==NULL) {        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     printf("Problem with prevalence resultfile: %s\n", fileresp);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     exit(0);  
   }      savm=oldm;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      oldm=newm;
   j1=0;      maxmax=0.;
        for(j=1;j<=nlstate;j++){
   j=cptcoveff;        min=1.;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        max=0.;
          for(i=1; i<=nlstate; i++) {
   for(k1=1; k1<=j;k1++){          sumnew=0;
     for(i1=1; i1<=ncodemax[k1];i1++){          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       j1++;          prlim[i][j]= newm[i][j]/(1-sumnew);
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          max=FMAX(max,prlim[i][j]);
         scanf("%d", i);*/          min=FMIN(min,prlim[i][j]);
       for (i=-1; i<=nlstate+ndeath; i++)          }
         for (jk=-1; jk<=nlstate+ndeath; jk++)          maxmin=max-min;
           for(m=agemin; m <= agemax+3; m++)        maxmax=FMAX(maxmax,maxmin);
             freq[i][jk][m]=0;      }
            if(maxmax < ftolpl){
       dateintsum=0;        return prlim;
       k2cpt=0;      }
       for (i=1; i<=imx; i++) {    }
         bool=1;  }
         if  (cptcovn>0) {  
           for (z1=1; z1<=cptcoveff; z1++)  /*************** transition probabilities ***************/ 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
               bool=0;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         }  {
         if (bool==1) {    double s1, s2;
           for(m=firstpass; m<=lastpass; m++){    /*double t34;*/
             k2=anint[m][i]+(mint[m][i]/12.);    int i,j,j1, nc, ii, jj;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  
               if(agev[m][i]==0) agev[m][i]=agemax+1;      for(i=1; i<= nlstate; i++){
               if(agev[m][i]==1) agev[m][i]=agemax+2;        for(j=1; j<i;j++){
               if (m<lastpass) {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];            /*s2 += param[i][j][nc]*cov[nc];*/
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
               }  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
                        }
               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;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        }
       }
       if  (cptcovn>0) {      /*ps[3][2]=1;*/
         fprintf(ficresp, "\n#********** Variable ");      
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      for(i=1; i<= nlstate; i++){
         fprintf(ficresp, "**********\n#");        s1=0;
       }        for(j=1; j<i; j++)
       for(i=1; i<=nlstate;i++)          s1+=exp(ps[i][j]);
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        for(j=i+1; j<=nlstate+ndeath; j++)
       fprintf(ficresp, "\n");          s1+=exp(ps[i][j]);
              ps[i][i]=1./(s1+1.);
       for(i=(int)agemin; i <= (int)agemax+3; i++){        for(j=1; j<i; j++)
         if(i==(int)agemax+3)          ps[i][j]= exp(ps[i][j])*ps[i][i];
           printf("Total");        for(j=i+1; j<=nlstate+ndeath; j++)
         else          ps[i][j]= exp(ps[i][j])*ps[i][i];
           printf("Age %d", i);        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         for(jk=1; jk <=nlstate ; jk++){      } /* end i */
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      
             pp[jk] += freq[jk][m][i];      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         }        for(jj=1; jj<= nlstate+ndeath; jj++){
         for(jk=1; jk <=nlstate ; jk++){          ps[ii][jj]=0;
           for(m=-1, pos=0; m <=0 ; m++)          ps[ii][ii]=1;
             pos += freq[jk][m][i];        }
           if(pp[jk]>=1.e-10)      }
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      
           else  
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
         }  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   /*         printf("ddd %lf ",ps[ii][jj]); */
         for(jk=1; jk <=nlstate ; jk++){  /*       } */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  /*       printf("\n "); */
             pp[jk] += freq[jk][m][i];  /*        } */
         }  /*        printf("\n ");printf("%lf ",cov[2]); */
          /*
         for(jk=1,pos=0; jk <=nlstate ; jk++)        for(i=1; i<= npar; i++) printf("%f ",x[i]);
           pos += pp[jk];        goto end;*/
         for(jk=1; jk <=nlstate ; jk++){      return ps;
           if(pos>=1.e-5)  }
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  
           else  /**************** Product of 2 matrices ******************/
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  
           if( i <= (int) agemax){  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
             if(pos>=1.e-5){  {
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
               probs[i][jk][j1]= pp[jk]/pos;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/    /* in, b, out are matrice of pointers which should have been initialized 
             }       before: only the contents of out is modified. The function returns
             else       a pointer to pointers identical to out */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    long i, j, k;
           }    for(i=nrl; i<= nrh; i++)
         }      for(k=ncolol; k<=ncoloh; k++)
                for(j=ncl,out[i][k]=0.; j<=nch; j++)
         for(jk=-1; jk <=nlstate+ndeath; jk++)          out[i][k] +=in[i][j]*b[j][k];
           for(m=-1; m <=nlstate+ndeath; m++)  
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    return out;
         if(i <= (int) agemax)  }
           fprintf(ficresp,"\n");  
         printf("\n");  
       }  /************* Higher Matrix Product ***************/
     }  
   }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   dateintmean=dateintsum/k2cpt;  {
      /* Computes the transition matrix starting at age 'age' over 
   fclose(ficresp);       'nhstepm*hstepm*stepm' months (i.e. until
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   free_vector(pp,1,nlstate);       nhstepm*hstepm matrices. 
         Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   /* End of Freq */       (typically every 2 years instead of every month which is too big 
 }       for the memory).
        Model is determined by parameters x and covariates have to be 
 /************ Prevalence ********************/       included manually here. 
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)  
 {  /* Some frequencies */       */
    
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    int i, j, d, h, k;
   double ***freq; /* Frequencies */    double **out, cov[NCOVMAX];
   double *pp;    double **newm;
   double pos, k2;  
     /* Hstepm could be zero and should return the unit matrix */
   pp=vector(1,nlstate);    for (i=1;i<=nlstate+ndeath;i++)
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (j=1;j<=nlstate+ndeath;j++){
          oldm[i][j]=(i==j ? 1.0 : 0.0);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        po[i][j][0]=(i==j ? 1.0 : 0.0);
   j1=0;      }
      /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   j=cptcoveff;    for(h=1; h <=nhstepm; h++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      for(d=1; d <=hstepm; d++){
          newm=savm;
  for(k1=1; k1<=j;k1++){        /* Covariates have to be included here again */
     for(i1=1; i1<=ncodemax[k1];i1++){        cov[1]=1.;
       j1++;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
          for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for (i=-1; i<=nlstate+ndeath; i++)          for (k=1; k<=cptcovage;k++)
         for (jk=-1; jk<=nlstate+ndeath; jk++)            cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for(m=agemin; m <= agemax+3; m++)        for (k=1; k<=cptcovprod;k++)
             freq[i][jk][m]=0;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
        
       for (i=1; i<=imx; i++) {  
         bool=1;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         if  (cptcovn>0) {        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
           for (z1=1; z1<=cptcoveff; z1++)        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])                     pmij(pmmij,cov,ncovmodel,x,nlstate));
               bool=0;        savm=oldm;
         }        oldm=newm;
         if (bool==1) {      }
           for(m=firstpass; m<=lastpass; m++){      for(i=1; i<=nlstate+ndeath; i++)
             k2=anint[m][i]+(mint[m][i]/12.);        for(j=1;j<=nlstate+ndeath;j++) {
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          po[i][j][h]=newm[i][j];
               if(agev[m][i]==0) agev[m][i]=agemax+1;          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
               if(agev[m][i]==1) agev[m][i]=agemax+2;        }
               if (m<lastpass)      /*printf("h=%d ",h);*/
                 if (calagedate>0) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    } /* end h */
               else  /*     printf("\n H=%d \n",h); */
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    return po;
                freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];  }
             }  
           }  
         }  /*************** log-likelihood *************/
       }  double func( double *x)
         for(i=(int)agemin; i <= (int)agemax+3; i++){  {
           for(jk=1; jk <=nlstate ; jk++){    int i, ii, j, k, mi, d, kk;
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
               pp[jk] += freq[jk][m][i];    double **out;
           }    double sw; /* Sum of weights */
           for(jk=1; jk <=nlstate ; jk++){    double lli; /* Individual log likelihood */
             for(m=-1, pos=0; m <=0 ; m++)    int s1, s2;
             pos += freq[jk][m][i];    double bbh, survp;
         }    long ipmx;
            /*extern weight */
          for(jk=1; jk <=nlstate ; jk++){    /* We are differentiating ll according to initial status */
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
              pp[jk] += freq[jk][m][i];    /*for(i=1;i<imx;i++) 
          }      printf(" %d\n",s[4][i]);
              */
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    cov[1]=1.;
   
          for(jk=1; jk <=nlstate ; jk++){              for(k=1; k<=nlstate; k++) ll[k]=0.;
            if( i <= (int) agemax){  
              if(pos>=1.e-5){    if(mle==1){
                probs[i][jk][j1]= pp[jk]/pos;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
              }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
            }        for(mi=1; mi<= wav[i]-1; mi++){
          }          for (ii=1;ii<=nlstate+ndeath;ii++)
                      for (j=1;j<=nlstate+ndeath;j++){
         }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            }
           for(d=0; d<dh[mi][i]; d++){
              newm=savm;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   free_vector(pp,1,nlstate);            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 }  /* End of Freq */            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 /************* Waves Concatenation ***************/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            oldm=newm;
 {          } /* end mult */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        
      Death is a valid wave (if date is known).          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          /* But now since version 0.9 we anticipate for bias at large stepm.
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]           * If stepm is larger than one month (smallest stepm) and if the exact delay 
      and mw[mi+1][i]. dh depends on stepm.           * (in months) between two waves is not a multiple of stepm, we rounded to 
      */           * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
   int i, mi, m;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;           * probability in order to take into account the bias as a fraction of the way
      double sum=0., jmean=0.;*/           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
   int j, k=0,jk, ju, jl;           * For stepm=1 the results are the same as for previous versions of Imach.
   double sum=0.;           * For stepm > 1 the results are less biased than in previous versions. 
   jmin=1e+5;           */
   jmax=-1;          s1=s[mw[mi][i]][i];
   jmean=0.;          s2=s[mw[mi+1][i]][i];
   for(i=1; i<=imx; i++){          bbh=(double)bh[mi][i]/(double)stepm; 
     mi=0;          /* bias bh is positive if real duration
     m=firstpass;           * is higher than the multiple of stepm and negative otherwise.
     while(s[m][i] <= nlstate){           */
       if(s[m][i]>=1)          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
         mw[++mi][i]=m;          if( s2 > nlstate){ 
       if(m >=lastpass)            /* i.e. if s2 is a death state and if the date of death is known 
         break;               then the contribution to the likelihood is the probability to 
       else               die between last step unit time and current  step unit time, 
         m++;               which is also equal to probability to die before dh 
     }/* end while */               minus probability to die before dh-stepm . 
     if (s[m][i] > nlstate){               In version up to 0.92 likelihood was computed
       mi++;     /* Death is another wave */          as if date of death was unknown. Death was treated as any other
       /* if(mi==0)  never been interviewed correctly before death */          health state: the date of the interview describes the actual state
          /* Only death is a correct wave */          and not the date of a change in health state. The former idea was
       mw[mi][i]=m;          to consider that at each interview the state was recorded
     }          (healthy, disable or death) and IMaCh was corrected; but when we
           introduced the exact date of death then we should have modified
     wav[i]=mi;          the contribution of an exact death to the likelihood. This new
     if(mi==0)          contribution is smaller and very dependent of the step unit
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          stepm. It is no more the probability to die between last interview
   }          and month of death but the probability to survive from last
           interview up to one month before death multiplied by the
   for(i=1; i<=imx; i++){          probability to die within a month. Thanks to Chris
     for(mi=1; mi<wav[i];mi++){          Jackson for correcting this bug.  Former versions increased
       if (stepm <=0)          mortality artificially. The bad side is that we add another loop
         dh[mi][i]=1;          which slows down the processing. The difference can be up to 10%
       else{          lower mortality.
         if (s[mw[mi+1][i]][i] > nlstate) {            */
           if (agedc[i] < 2*AGESUP) {            lli=log(out[s1][s2] - savm[s1][s2]);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  
           if(j==0) j=1;  /* Survives at least one month after exam */  
           k=k+1;          } else if  (s2==-2) {
           if (j >= jmax) jmax=j;            for (j=1,survp=0. ; j<=nlstate; j++) 
           if (j <= jmin) jmin=j;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           sum=sum+j;            /*survp += out[s1][j]; */
           /*if (j<0) printf("j=%d num=%d \n",j,i); */            lli= log(survp);
           }          }
         }          
         else{          else if  (s2==-4) { 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            for (j=3,survp=0. ; j<=nlstate; j++)  
           k=k+1;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           if (j >= jmax) jmax=j;            lli= log(survp); 
           else if (j <= jmin)jmin=j;          } 
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  
           sum=sum+j;          else if  (s2==-5) { 
         }            for (j=1,survp=0. ; j<=2; j++)  
         jk= j/stepm;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         jl= j -jk*stepm;            lli= log(survp); 
         ju= j -(jk+1)*stepm;          } 
         if(jl <= -ju)          
           dh[mi][i]=jk;          else{
         else            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           dh[mi][i]=jk+1;            /*  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(dh[mi][i]==0)          } 
           dh[mi][i]=1; /* At least one step */          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       }          /*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); */
   }          ipmx +=1;
   jmean=sum/k;          sw += weight[i];
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
  }        } /* end of wave */
 /*********** Tricode ****************************/      } /* end of individual */
 void tricode(int *Tvar, int **nbcode, int imx)    }  else if(mle==2){
 {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int Ndum[20],ij=1, k, j, i;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int cptcode=0;        for(mi=1; mi<= wav[i]-1; mi++){
   cptcoveff=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   for (k=0; k<19; k++) Ndum[k]=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (k=1; k<=7; k++) ncodemax[k]=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          for(d=0; d<=dh[mi][i]; d++){
     for (i=1; i<=imx; i++) {            newm=savm;
       ij=(int)(covar[Tvar[j]][i]);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       Ndum[ij]++;            for (kk=1; kk<=cptcovage;kk++) {
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       if (ij > cptcode) cptcode=ij;            }
     }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (i=0; i<=cptcode; i++) {            savm=oldm;
       if(Ndum[i]!=0) ncodemax[j]++;            oldm=newm;
     }          } /* end mult */
     ij=1;        
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
     for (i=1; i<=ncodemax[j]; i++) {          bbh=(double)bh[mi][i]/(double)stepm; 
       for (k=0; k<=19; k++) {          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         if (Ndum[k] != 0) {          ipmx +=1;
           nbcode[Tvar[j]][ij]=k;          sw += weight[i];
                    ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           ij++;        } /* end of wave */
         }      } /* end of individual */
         if (ij > ncodemax[j]) break;    }  else if(mle==3){  /* exponential inter-extrapolation */
       }        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 (k=0; k<19; k++) Ndum[k]=0;            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  for (i=1; i<=ncovmodel-2; i++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       ij=Tvar[i];            }
       Ndum[ij]++;          for(d=0; d<dh[mi][i]; d++){
     }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
  ij=1;            for (kk=1; kk<=cptcovage;kk++) {
  for (i=1; i<=10; i++) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
    if((Ndum[i]!=0) && (i<=ncovcol)){            }
      Tvaraff[ij]=i;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      ij++;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
    }            savm=oldm;
  }            oldm=newm;
            } /* end mult */
     cptcoveff=ij-1;        
 }          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 /*********** Health Expectancies ****************/          bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )          ipmx +=1;
           sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* Health expectancies */        } /* end of wave */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;      } /* end of individual */
   double age, agelim, hf;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   double ***p3mat,***varhe;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double **dnewm,**doldm;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double *xp;        for(mi=1; mi<= wav[i]-1; mi++){
   double **gp, **gm;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double ***gradg, ***trgradg;            for (j=1;j<=nlstate+ndeath;j++){
   int theta;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);            }
   xp=vector(1,npar);          for(d=0; d<dh[mi][i]; d++){
   dnewm=matrix(1,nlstate*2,1,npar);            newm=savm;
   doldm=matrix(1,nlstate*2,1,nlstate*2);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
   fprintf(ficreseij,"# Health expectancies\n");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   fprintf(ficreseij,"# Age");            }
   for(i=1; i<=nlstate;i++)          
     for(j=1; j<=nlstate;j++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       fprintf(ficreseij," %1d-%1d (SE)",i,j);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   fprintf(ficreseij,"\n");            savm=oldm;
             oldm=newm;
   if(estepm < stepm){          } /* end mult */
     printf ("Problem %d lower than %d\n",estepm, stepm);        
   }          s1=s[mw[mi][i]][i];
   else  hstepm=estepm;            s2=s[mw[mi+1][i]][i];
   /* We compute the life expectancy from trapezoids spaced every estepm months          if( s2 > nlstate){ 
    * This is mainly to measure the difference between two models: for example            lli=log(out[s1][s2] - savm[s1][s2]);
    * 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            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
    * progression inbetween and thus overestimating or underestimating according          }
    * to the curvature of the survival function. If, for the same date, we          ipmx +=1;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months          sw += weight[i];
    * to compare the new estimate of Life expectancy with the same linear          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
    * hypothesis. A more precise result, taking into account a more precise  /*      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]); */
    * curvature will be obtained if estepm is as small as stepm. */        } /* end of wave */
       } /* end of individual */
   /* For example we decided to compute the life expectancy with the smallest unit */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      nhstepm is the number of hstepm from age to agelim        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      nstepm is the number of stepm from age to agelin.        for(mi=1; mi<= wav[i]-1; mi++){
      Look at hpijx to understand the reason of that which relies in memory size          for (ii=1;ii<=nlstate+ndeath;ii++)
      and note for a fixed period like estepm months */            for (j=1;j<=nlstate+ndeath;j++){
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      survival function given by stepm (the optimization length). Unfortunately it              savm[ii][j]=(ii==j ? 1.0 : 0.0);
      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          for(d=0; d<dh[mi][i]; d++){
      results. So we changed our mind and took the option of the best precision.            newm=savm;
   */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   agelim=AGESUP;            }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          
     /* nhstepm age range expressed in number of stepm */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     nstepm=(int) rint((agelim-age)*YEARM/stepm);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */            savm=oldm;
     /* if (stepm >= YEARM) hstepm=1;*/            oldm=newm;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          } /* end mult */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);          s1=s[mw[mi][i]][i];
     gp=matrix(0,nhstepm,1,nlstate*2);          s2=s[mw[mi+1][i]][i];
     gm=matrix(0,nhstepm,1,nlstate*2);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          sw += weight[i];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
          } /* end of wave */
       } /* end of individual */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    } /* End of if */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* Computing Variances of health expectancies */    /* 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 */
      for(theta=1; theta <=npar; theta++){    return -l;
       for(i=1; i<=npar; i++){  }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }  /*************** log-likelihood *************/
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    double funcone( double *x)
    {
       cptj=0;    /* Same as likeli but slower because of a lot of printf and if */
       for(j=1; j<= nlstate; j++){    int i, ii, j, k, mi, d, kk;
         for(i=1; i<=nlstate; i++){    double l, ll[NLSTATEMAX], cov[NCOVMAX];
           cptj=cptj+1;    double **out;
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    double lli; /* Individual log likelihood */
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    double llt;
           }    int s1, s2;
         }    double bbh, survp;
       }    /*extern weight */
          /* We are differentiating ll according to initial status */
          /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       for(i=1; i<=npar; i++)    /*for(i=1;i<imx;i++) 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      printf(" %d\n",s[4][i]);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      */
          cov[1]=1.;
       cptj=0;  
       for(j=1; j<= nlstate; j++){    for(k=1; k<=nlstate; k++) ll[k]=0.;
         for(i=1;i<=nlstate;i++){  
           cptj=cptj+1;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      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);
                  savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
         for(d=0; d<dh[mi][i]; d++){
       for(j=1; j<= nlstate*2; j++)          newm=savm;
         for(h=0; h<=nhstepm-1; h++){          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          for (kk=1; kk<=cptcovage;kk++) {
         }            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           }
      }          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 /* End theta */          savm=oldm;
           oldm=newm;
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);        } /* end mult */
         
      for(h=0; h<=nhstepm-1; h++)        s1=s[mw[mi][i]][i];
       for(j=1; j<=nlstate*2;j++)        s2=s[mw[mi+1][i]][i];
         for(theta=1; theta <=npar; theta++)        bbh=(double)bh[mi][i]/(double)stepm; 
         trgradg[h][j][theta]=gradg[h][theta][j];        /* bias is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.
          */
      for(i=1;i<=nlstate*2;i++)        if( s2 > nlstate && (mle <5) ){  /* Jackson */
       for(j=1;j<=nlstate*2;j++)          lli=log(out[s1][s2] - savm[s1][s2]);
         varhe[i][j][(int)age] =0.;        } else if  (s2==-2) {
           for (j=1,survp=0. ; j<=nlstate; j++) 
     for(h=0;h<=nhstepm-1;h++){            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       for(k=0;k<=nhstepm-1;k++){          lli= log(survp);
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);        }else if (mle==1){
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         for(i=1;i<=nlstate*2;i++)        } else if(mle==2){
           for(j=1;j<=nlstate*2;j++)          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;        } else if(mle==3){  /* exponential inter-extrapolation */
       }          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     }        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           lli=log(out[s1][s2]); /* Original formula */
              } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
     /* Computing expectancies */          lli=log(out[s1][s2]); /* Original formula */
     for(i=1; i<=nlstate;i++)        } /* End of if */
       for(j=1; j<=nlstate;j++)        ipmx +=1;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){        sw += weight[i];
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;        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]); */
 /* 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(globpr){
           fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
         }   %11.6f %11.6f %11.6f ", \
                   num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     fprintf(ficreseij,"%3.0f",age );                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     cptj=0;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     for(i=1; i<=nlstate;i++)            llt +=ll[k]*gipmx/gsw;
       for(j=1; j<=nlstate;j++){            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
         cptj++;          }
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );          fprintf(ficresilk," %10.6f\n", -llt);
       }        }
     fprintf(ficreseij,"\n");      } /* end of wave */
        } /* end of individual */
     free_matrix(gm,0,nhstepm,1,nlstate*2);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     free_matrix(gp,0,nhstepm,1,nlstate*2);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);    if(globpr==0){ /* First time we count the contributions and weights */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      gipmx=ipmx;
   }      gsw=sw;
   free_vector(xp,1,npar);    }
   free_matrix(dnewm,1,nlstate*2,1,npar);    return -l;
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);  }
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);  
 }  
   /*************** function likelione ***********/
 /************ Variance ******************/  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)  {
 {    /* This routine should help understanding what is done with 
   /* Variance of health expectancies */       the selection of individuals/waves and
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/       to check the exact contribution to the likelihood.
   double **newm;       Plotting could be done.
   double **dnewm,**doldm;     */
   int i, j, nhstepm, hstepm, h, nstepm ;    int k;
   int k, cptcode;  
   double *xp;    if(*globpri !=0){ /* Just counts and sums, no printings */
   double **gp, **gm;      strcpy(fileresilk,"ilk"); 
   double ***gradg, ***trgradg;      strcat(fileresilk,fileres);
   double ***p3mat;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   double age,agelim, hf;        printf("Problem with resultfile: %s\n", fileresilk);
   int theta;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
    fprintf(ficresvij,"# Covariances of life expectancies\n");      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(ficresvij,"# Age");      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   for(i=1; i<=nlstate;i++)      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     for(j=1; j<=nlstate;j++)      for(k=1; k<=nlstate; k++) 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   fprintf(ficresvij,"\n");      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);    *fretone=(*funcone)(p);
   doldm=matrix(1,nlstate,1,nlstate);    if(*globpri !=0){
        fclose(ficresilk);
   if(estepm < stepm){      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     printf ("Problem %d lower than %d\n",estepm, stepm);      fflush(fichtm); 
   }    } 
   else  hstepm=estepm;      return;
   /* For example we decided to compute the life expectancy with the smallest unit */  }
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.  
      nhstepm is the number of hstepm from age to agelim  
      nstepm is the number of stepm from age to agelin.  /*********** Maximum Likelihood Estimation ***************/
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like k years */  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   /* 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    int i,j, iter;
      means that if the survival funtion is printed only each two years of age and if    double **xi;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    double fret;
      results. So we changed our mind and took the option of the best precision.    double fretone; /* Only one call to likelihood */
   */    /*  char filerespow[FILENAMELENGTH];*/
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    xi=matrix(1,npar,1,npar);
   agelim = AGESUP;    for (i=1;i<=npar;i++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (j=1;j<=npar;j++)
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        xi[i][j]=(i==j ? 1.0 : 0.0);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    strcpy(filerespow,"pow"); 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    strcat(filerespow,fileres);
     gp=matrix(0,nhstepm,1,nlstate);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     gm=matrix(0,nhstepm,1,nlstate);      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     for(theta=1; theta <=npar; theta++){    }
       for(i=1; i<=npar; i++){ /* Computes gradient */    fprintf(ficrespow,"# Powell\n# iter -2*LL");
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    for (i=1;i<=nlstate;i++)
       }      for(j=1;j<=nlstate+ndeath;j++)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    fprintf(ficrespow,"\n");
   
       if (popbased==1) {    powell(p,xi,npar,ftol,&iter,&fret,func);
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];    free_matrix(xi,1,npar,1,npar);
       }    fclose(ficrespow);
      printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       for(j=1; j<= nlstate; j++){    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         for(h=0; h<=nhstepm; h++){    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  }
         }  
       }  /**** Computes Hessian and covariance matrix ***/
      void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       for(i=1; i<=npar; i++) /* Computes gradient */  {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double  **a,**y,*x,pd;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      double **hess;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int i, j,jk;
      int *indx;
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
           prlim[i][i]=probs[(int)age][i][ij];    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
       }    void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
       for(j=1; j<= nlstate; j++){    double gompertz(double p[]);
         for(h=0; h<=nhstepm; h++){    hess=matrix(1,npar,1,npar);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    printf("\nCalculation of the hessian matrix. Wait...\n");
         }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       }    for (i=1;i<=npar;i++){
       printf("%d",i);fflush(stdout);
       for(j=1; j<= nlstate; j++)      fprintf(ficlog,"%d",i);fflush(ficlog);
         for(h=0; h<=nhstepm; h++){     
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
         }      
     } /* End theta */      /*  printf(" %f ",p[i]);
           printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    }
     
     for(h=0; h<=nhstepm; h++)    for (i=1;i<=npar;i++) {
       for(j=1; j<=nlstate;j++)      for (j=1;j<=npar;j++)  {
         for(theta=1; theta <=npar; theta++)        if (j>i) { 
           trgradg[h][j][theta]=gradg[h][theta][j];          printf(".%d%d",i,j);fflush(stdout);
           fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          hess[i][j]=hessij(p,delti,i,j,func,npar);
     for(i=1;i<=nlstate;i++)          
       for(j=1;j<=nlstate;j++)          hess[j][i]=hess[i][j];    
         vareij[i][j][(int)age] =0.;          /*printf(" %lf ",hess[i][j]);*/
         }
     for(h=0;h<=nhstepm;h++){      }
       for(k=0;k<=nhstepm;k++){    }
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    printf("\n");
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    fprintf(ficlog,"\n");
         for(i=1;i<=nlstate;i++)  
           for(j=1;j<=nlstate;j++)    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       }    
     }    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
     fprintf(ficresvij,"%.0f ",age );    x=vector(1,npar);
     for(i=1; i<=nlstate;i++)    indx=ivector(1,npar);
       for(j=1; j<=nlstate;j++){    for (i=1;i<=npar;i++)
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       }    ludcmp(a,npar,indx,&pd);
     fprintf(ficresvij,"\n");  
     free_matrix(gp,0,nhstepm,1,nlstate);    for (j=1;j<=npar;j++) {
     free_matrix(gm,0,nhstepm,1,nlstate);      for (i=1;i<=npar;i++) x[i]=0;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      x[j]=1;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      lubksb(a,npar,indx,x);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (i=1;i<=npar;i++){ 
   } /* End age */        matcov[i][j]=x[i];
        }
   free_vector(xp,1,npar);    }
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);    printf("\n#Hessian matrix#\n");
     fprintf(ficlog,"\n#Hessian matrix#\n");
 }    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
 /************ Variance of prevlim ******************/        printf("%.3e ",hess[i][j]);
 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)        fprintf(ficlog,"%.3e ",hess[i][j]);
 {      }
   /* Variance of prevalence limit */      printf("\n");
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      fprintf(ficlog,"\n");
   double **newm;    }
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm;    /* Recompute Inverse */
   int k, cptcode;    for (i=1;i<=npar;i++)
   double *xp;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   double *gp, *gm;    ludcmp(a,npar,indx,&pd);
   double **gradg, **trgradg;  
   double age,agelim;    /*  printf("\n#Hessian matrix recomputed#\n");
   int theta;  
        for (j=1;j<=npar;j++) {
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      for (i=1;i<=npar;i++) x[i]=0;
   fprintf(ficresvpl,"# Age");      x[j]=1;
   for(i=1; i<=nlstate;i++)      lubksb(a,npar,indx,x);
       fprintf(ficresvpl," %1d-%1d",i,i);      for (i=1;i<=npar;i++){ 
   fprintf(ficresvpl,"\n");        y[i][j]=x[i];
         printf("%.3e ",y[i][j]);
   xp=vector(1,npar);        fprintf(ficlog,"%.3e ",y[i][j]);
   dnewm=matrix(1,nlstate,1,npar);      }
   doldm=matrix(1,nlstate,1,nlstate);      printf("\n");
        fprintf(ficlog,"\n");
   hstepm=1*YEARM; /* Every year of age */    }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    */
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    free_matrix(a,1,npar,1,npar);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    free_matrix(y,1,npar,1,npar);
     if (stepm >= YEARM) hstepm=1;    free_vector(x,1,npar);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    free_ivector(indx,1,npar);
     gradg=matrix(1,npar,1,nlstate);    free_matrix(hess,1,npar,1,npar);
     gp=vector(1,nlstate);  
     gm=vector(1,nlstate);  
   }
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */  /*************** hessian matrix ****************/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
       }  {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int i;
       for(i=1;i<=nlstate;i++)    int l=1, lmax=20;
         gp[i] = prlim[i][i];    double k1,k2;
        double p2[NPARMAX+1];
       for(i=1; i<=npar; i++) /* Computes gradient */    double res;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double fx;
       for(i=1;i<=nlstate;i++)    int k=0,kmax=10;
         gm[i] = prlim[i][i];    double l1;
   
       for(i=1;i<=nlstate;i++)    fx=func(x);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    for (i=1;i<=npar;i++) p2[i]=x[i];
     } /* End theta */    for(l=0 ; l <=lmax; l++){
       l1=pow(10,l);
     trgradg =matrix(1,nlstate,1,npar);      delts=delt;
       for(k=1 ; k <kmax; k=k+1){
     for(j=1; j<=nlstate;j++)        delt = delta*(l1*k);
       for(theta=1; theta <=npar; theta++)        p2[theta]=x[theta] +delt;
         trgradg[j][theta]=gradg[theta][j];        k1=func(p2)-fx;
         p2[theta]=x[theta]-delt;
     for(i=1;i<=nlstate;i++)        k2=func(p2)-fx;
       varpl[i][(int)age] =0.;        /*res= (k1-2.0*fx+k2)/delt/delt; */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        
     for(i=1;i<=nlstate;i++)  #ifdef DEBUG
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        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);
     fprintf(ficresvpl,"%.0f ",age );  #endif
     for(i=1; i<=nlstate;i++)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     fprintf(ficresvpl,"\n");          k=kmax;
     free_vector(gp,1,nlstate);        }
     free_vector(gm,1,nlstate);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     free_matrix(gradg,1,npar,1,nlstate);          k=kmax; l=lmax*10.;
     free_matrix(trgradg,1,nlstate,1,npar);        }
   } /* End age */        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
   free_vector(xp,1,npar);        }
   free_matrix(doldm,1,nlstate,1,npar);      }
   free_matrix(dnewm,1,nlstate,1,nlstate);    }
     delti[theta]=delts;
 }    return res; 
     
 /************ Variance of one-step probabilities  ******************/  }
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)  
 {  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   int i, j, i1, k1, j1, z1;  {
   int k=0, cptcode;    int i;
   double **dnewm,**doldm;    int l=1, l1, lmax=20;
   double *xp;    double k1,k2,k3,k4,res,fx;
   double *gp, *gm;    double p2[NPARMAX+1];
   double **gradg, **trgradg;    int k;
   double age,agelim, cov[NCOVMAX];  
   int theta;    fx=func(x);
   char fileresprob[FILENAMELENGTH];    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
   strcpy(fileresprob,"prob");      p2[thetai]=x[thetai]+delti[thetai]/k;
   strcat(fileresprob,fileres);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      k1=func(p2)-fx;
     printf("Problem with resultfile: %s\n", fileresprob);    
   }      p2[thetai]=x[thetai]+delti[thetai]/k;
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
        k2=func(p2)-fx;
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");    
   fprintf(ficresprob,"# Age");      p2[thetai]=x[thetai]-delti[thetai]/k;
   for(i=1; i<=nlstate;i++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     for(j=1; j<=(nlstate+ndeath);j++)      k3=func(p2)-fx;
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    
       p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   fprintf(ficresprob,"\n");      k4=func(p2)-fx;
       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
   xp=vector(1,npar);      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);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      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);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));  #endif
      }
   cov[1]=1;    return res;
   j=cptcoveff;  }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  
   j1=0;  /************** Inverse of matrix **************/
   for(k1=1; k1<=1;k1++){  void ludcmp(double **a, int n, int *indx, double *d) 
     for(i1=1; i1<=ncodemax[k1];i1++){  { 
     j1++;    int i,imax,j,k; 
     double big,dum,sum,temp; 
     if  (cptcovn>0) {    double *vv; 
       fprintf(ficresprob, "\n#********** Variable ");   
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    vv=vector(1,n); 
       fprintf(ficresprob, "**********\n#");    *d=1.0; 
     }    for (i=1;i<=n;i++) { 
          big=0.0; 
       for (age=bage; age<=fage; age ++){      for (j=1;j<=n;j++) 
         cov[2]=age;        if ((temp=fabs(a[i][j])) > big) big=temp; 
         for (k=1; k<=cptcovn;k++) {      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];      vv[i]=1.0/big; 
              } 
         }    for (j=1;j<=n;j++) { 
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      for (i=1;i<j;i++) { 
         for (k=1; k<=cptcovprod;k++)        sum=a[i][j]; 
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
                a[i][j]=sum; 
         gradg=matrix(1,npar,1,9);      } 
         trgradg=matrix(1,9,1,npar);      big=0.0; 
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      for (i=j;i<=n;i++) { 
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        sum=a[i][j]; 
            for (k=1;k<j;k++) 
         for(theta=1; theta <=npar; theta++){          sum -= a[i][k]*a[k][j]; 
           for(i=1; i<=npar; i++)        a[i][j]=sum; 
             xp[i] = x[i] + (i==theta ?delti[theta]:0);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
                    big=dum; 
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          imax=i; 
                  } 
           k=0;      } 
           for(i=1; i<= (nlstate+ndeath); i++){      if (j != imax) { 
             for(j=1; j<=(nlstate+ndeath);j++){        for (k=1;k<=n;k++) { 
               k=k+1;          dum=a[imax][k]; 
               gp[k]=pmmij[i][j];          a[imax][k]=a[j][k]; 
             }          a[j][k]=dum; 
           }        } 
                  *d = -(*d); 
           for(i=1; i<=npar; i++)        vv[imax]=vv[j]; 
             xp[i] = x[i] - (i==theta ?delti[theta]:0);      } 
          indx[j]=imax; 
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      if (a[j][j] == 0.0) a[j][j]=TINY; 
           k=0;      if (j != n) { 
           for(i=1; i<=(nlstate+ndeath); i++){        dum=1.0/(a[j][j]); 
             for(j=1; j<=(nlstate+ndeath);j++){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
               k=k+1;      } 
               gm[k]=pmmij[i][j];    } 
             }    free_vector(vv,1,n);  /* Doesn't work */
           }  ;
        } 
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)  
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    void lubksb(double **a, int n, int *indx, double b[]) 
         }  { 
     int i,ii=0,ip,j; 
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    double sum; 
           for(theta=1; theta <=npar; theta++)   
             trgradg[j][theta]=gradg[theta][j];    for (i=1;i<=n;i++) { 
              ip=indx[i]; 
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      sum=b[ip]; 
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);      b[ip]=b[i]; 
              if (ii) 
         pmij(pmmij,cov,ncovmodel,x,nlstate);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
              else if (sum) ii=i; 
         k=0;      b[i]=sum; 
         for(i=1; i<=(nlstate+ndeath); i++){    } 
           for(j=1; j<=(nlstate+ndeath);j++){    for (i=n;i>=1;i--) { 
             k=k+1;      sum=b[i]; 
             gm[k]=pmmij[i][j];      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
           }      b[i]=sum/a[i][i]; 
         }    } 
        } 
      /*printf("\n%d ",(int)age);  
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){  void pstamp(FILE *fichier)
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));  {
      }*/    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   }
         fprintf(ficresprob,"\n%d ",(int)age);  
   /************ Frequencies ********************/
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)  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[])
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));  {  /* Some frequencies */
      
       }    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     }    int first;
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    double ***freq; /* Frequencies */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    double *pp, **prop;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    char fileresp[FILENAMELENGTH];
   }    
   free_vector(xp,1,npar);    pp=vector(1,nlstate);
   fclose(ficresprob);    prop=matrix(1,nlstate,iagemin,iagemax+3);
      strcpy(fileresp,"p");
 }    strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
 /******************* Printing html file ***********/      printf("Problem with prevalence resultfile: %s\n", fileresp);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
  int lastpass, int stepm, int weightopt, char model[],\      exit(0);
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \    }
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
  char version[], int popforecast, int estepm ){    j1=0;
   int jj1, k1, i1, cpt;    
   FILE *fichtm;    j=cptcoveff;
   /*char optionfilehtm[FILENAMELENGTH];*/    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
   strcpy(optionfilehtm,optionfile);    first=1;
   strcat(optionfilehtm,".htm");  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    for(k1=1; k1<=j;k1++){
     printf("Problem with %s \n",optionfilehtm), exit(0);      for(i1=1; i1<=ncodemax[k1];i1++){
   }        j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n          scanf("%d", i);*/
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n        for (i=-5; i<=nlstate+ndeath; i++)  
 \n          for (jk=-5; jk<=nlstate+ndeath; jk++)  
 Total number of observations=%d <br>\n            for(m=iagemin; m <= iagemax+3; m++)
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n              freq[i][jk][m]=0;
 <hr  size=\"2\" color=\"#EC5E5E\">  
  <ul><li>Outputs files<br>\n      for (i=1; i<=nlstate; i++)  
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n        for(m=iagemin; m <= iagemax+3; m++)
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n          prop[i][m]=0;
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n        dateintsum=0;
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n        k2cpt=0;
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);        for (i=1; i<=imx; i++) {
           bool=1;
  fprintf(fichtm,"\n          if  (cptcovn>0) {
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n            for (z1=1; z1<=cptcoveff; z1++) 
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n                bool=0;
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n          }
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);          if (bool==1){
             for(m=firstpass; m<=lastpass; m++){
  if(popforecast==1) fprintf(fichtm,"\n              k2=anint[m][i]+(mint[m][i]/12.);
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         <br>",fileres,fileres,fileres,fileres);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
  else                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
    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);                if (m<lastpass) {
 fprintf(fichtm," <li>Graphs</li><p>");                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                   freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
  m=cptcoveff;                }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
  jj1=0;                  dateintsum=dateintsum+k2;
  for(k1=1; k1<=m;k1++){                  k2cpt++;
    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\">");        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
        }        pstamp(ficresp);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>        if  (cptcovn>0) {
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              fprintf(ficresp, "\n#********** Variable "); 
        for(cpt=1; cpt<nlstate;cpt++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>          fprintf(ficresp, "**********\n#");
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        }
        }        for(i=1; i<=nlstate;i++) 
     for(cpt=1; cpt<=nlstate;cpt++) {          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        fprintf(ficresp, "\n");
 interval) in state (%d): v%s%d%d.gif <br>        
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          for(i=iagemin; i <= iagemax+3; i++){
      }          if(i==iagemax+3){
      for(cpt=1; cpt<=nlstate;cpt++) {            fprintf(ficlog,"Total");
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>          }else{
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            if(first==1){
      }              first=0;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and              printf("See log file for details...\n");
 health expectancies in states (1) and (2): e%s%d.gif<br>            }
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            fprintf(ficlog,"Age %d", i);
 fprintf(fichtm,"\n</body>");          }
    }          for(jk=1; jk <=nlstate ; jk++){
    }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
 fclose(fichtm);              pp[jk] += freq[jk][m][i]; 
 }          }
           for(jk=1; jk <=nlstate ; jk++){
 /******************* Gnuplot file **************/            for(m=-1, pos=0; m <=0 ; m++)
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   strcpy(optionfilegnuplot,optionfilefiname);              }
   strcat(optionfilegnuplot,".gp.txt");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {            }else{
     printf("Problem with file %s",optionfilegnuplot);              if(first==1)
   }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 #ifdef windows            }
     fprintf(ficgp,"cd \"%s\" \n",pathc);          }
 #endif  
 m=pow(2,cptcoveff);          for(jk=1; jk <=nlstate ; jk++){
              for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
  /* 1eme*/              pp[jk] += freq[jk][m][i];
   for (cpt=1; cpt<= nlstate ; cpt ++) {          }       
    for (k1=1; k1<= m ; k1 ++) {          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
 #ifdef windows            posprop += prop[jk][i];
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);          }
 #endif          for(jk=1; jk <=nlstate ; jk++){
 #ifdef unix            if(pos>=1.e-5){
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);              if(first==1)
 #endif                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);
 for (i=1; i<= nlstate ; i ++) {            }else{
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              if(first==1)
   else fprintf(ficgp," \%%*lf (\%%*lf)");                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);            }
     for (i=1; i<= nlstate ; i ++) {            if( i <= iagemax){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              if(pos>=1.e-5){
   else fprintf(ficgp," \%%*lf (\%%*lf)");                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
 }                /*probs[i][jk][j1]= pp[jk]/pos;*/
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
      for (i=1; i<= nlstate ; i ++) {              }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              else
   else fprintf(ficgp," \%%*lf (\%%*lf)");                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
 }              }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          }
 #ifdef unix          
 fprintf(ficgp,"\nset ter gif small size 400,300");          for(jk=-1; jk <=nlstate+ndeath; jk++)
 #endif            for(m=-1; m <=nlstate+ndeath; m++)
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              if(freq[jk][m][i] !=0 ) {
    }              if(first==1)
   }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   /*2 eme*/                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
   for (k1=1; k1<= m ; k1 ++) {          if(i <= iagemax)
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);            fprintf(ficresp,"\n");
              if(first==1)
     for (i=1; i<= nlstate+1 ; i ++) {            printf("Others in log...\n");
       k=2*i;          fprintf(ficlog,"\n");
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        }
       for (j=1; j<= nlstate+1 ; j ++) {      }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    dateintmean=dateintsum/k2cpt; 
 }     
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    fclose(ficresp);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    free_vector(pp,1,nlstate);
       for (j=1; j<= nlstate+1 ; j ++) {    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /* End of Freq */
         else fprintf(ficgp," \%%*lf (\%%*lf)");  }
 }    
       fprintf(ficgp,"\" t\"\" w l 0,");  /************ Prevalence ********************/
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
       for (j=1; j<= nlstate+1 ; j ++) {  {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   else fprintf(ficgp," \%%*lf (\%%*lf)");       in each health status at the date of interview (if between dateprev1 and dateprev2).
 }         We still use firstpass and lastpass as another selection.
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    */
       else fprintf(ficgp,"\" t\"\" w l 0,");   
     }    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    double ***freq; /* Frequencies */
   }    double *pp, **prop;
      double pos,posprop; 
   /*3eme*/    double  y2; /* in fractional years */
     int iagemin, iagemax;
   for (k1=1; k1<= m ; k1 ++) {  
     for (cpt=1; cpt<= nlstate ; cpt ++) {    iagemin= (int) agemin;
       k=2+nlstate*(2*cpt-2);    iagemax= (int) agemax;
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    /*pp=vector(1,nlstate);*/
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    j1=0;
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    j=cptcoveff;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
 */    for(k1=1; k1<=j;k1++){
       for (i=1; i< nlstate ; i ++) {      for(i1=1; i1<=ncodemax[k1];i1++){
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);        j1++;
         
       }        for (i=1; i<=nlstate; i++)  
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          for(m=iagemin; m <= iagemax+3; m++)
     }            prop[i][m]=0.0;
     }       
          for (i=1; i<=imx; i++) { /* Each individual */
   /* CV preval stat */          bool=1;
     for (k1=1; k1<= m ; k1 ++) {          if  (cptcovn>0) {
     for (cpt=1; cpt<nlstate ; cpt ++) {            for (z1=1; z1<=cptcoveff; z1++) 
       k=3;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);                bool=0;
           } 
       for (i=1; i< nlstate ; i ++)          if (bool==1) { 
         fprintf(ficgp,"+$%d",k+i+1);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                    if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       l=3+(nlstate+ndeath)*cpt;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       for (i=1; i< nlstate ; i ++) {                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
         l=3+(nlstate+ndeath)*cpt;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
         fprintf(ficgp,"+$%d",l+i+1);                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
       }                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                    prop[s[m][i]][iagemax+3] += weight[i]; 
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                } 
     }              }
   }              } /* end selection of waves */
            }
   /* proba elementaires */        }
    for(i=1,jk=1; i <=nlstate; i++){        for(i=iagemin; i <= iagemax+3; i++){  
     for(k=1; k <=(nlstate+ndeath); k++){          
       if (k != i) {          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         for(j=1; j <=ncovmodel; j++){            posprop += prop[jk][i]; 
                  } 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  
           jk++;          for(jk=1; jk <=nlstate ; jk++){     
           fprintf(ficgp,"\n");            if( i <=  iagemax){ 
         }              if(posprop>=1.e-5){ 
       }                probs[i][jk][j1]= prop[jk][i]/posprop;
     }              } else
     }                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
             } 
     for(jk=1; jk <=m; jk++) {          }/* end jk */ 
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);        }/* end i */ 
    i=1;      } /* end i1 */
    for(k2=1; k2<=nlstate; k2++) {    } /* end k1 */
      k3=i;    
      for(k=1; k<=(nlstate+ndeath); k++) {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
        if (k != k2){    /*free_vector(pp,1,nlstate);*/
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
 ij=1;  }  /* End of prevalence */
         for(j=3; j <=ncovmodel; j++) {  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  /************* Waves Concatenation ***************/
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
           }  {
           else    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);       Death is a valid wave (if date is known).
         }       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
           fprintf(ficgp,")/(1");       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
               and mw[mi+1][i]. dh depends on stepm.
         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;    int i, mi, m;
           for(j=3; j <=ncovmodel; j++){    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {       double sum=0., jmean=0.;*/
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    int first;
             ij++;    int j, k=0,jk, ju, jl;
           }    double sum=0.;
           else    first=0;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    jmin=1e+5;
           }    jmax=-1;
           fprintf(ficgp,")");    jmean=0.;
         }    for(i=1; i<=imx; i++){
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      mi=0;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      m=firstpass;
         i=i+ncovmodel;      while(s[m][i] <= nlstate){
        }        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
      }          mw[++mi][i]=m;
    }        if(m >=lastpass)
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);          break;
    }        else
              m++;
   fclose(ficgp);      }/* end while */
 }  /* end gnuplot */      if (s[m][i] > nlstate){
         mi++;     /* Death is another wave */
         /* if(mi==0)  never been interviewed correctly before death */
 /*************** Moving average **************/           /* Only death is a correct wave */
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){        mw[mi][i]=m;
       }
   int i, cpt, cptcod;  
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)      wav[i]=mi;
       for (i=1; i<=nlstate;i++)      if(mi==0){
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        nbwarn++;
           mobaverage[(int)agedeb][i][cptcod]=0.;        if(first==0){
              printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          first=1;
       for (i=1; i<=nlstate;i++){        }
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        if(first==1){
           for (cpt=0;cpt<=4;cpt++){          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        }
           }      } /* end mi==0 */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    } /* End individuals */
         }  
       }    for(i=1; i<=imx; i++){
     }      for(mi=1; mi<wav[i];mi++){
            if (stepm <=0)
 }          dh[mi][i]=1;
         else{
           if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
 /************** Forecasting ******************/            if (agedc[i] < 2*AGESUP) {
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                if(j==0) j=1;  /* Survives at least one month after exam */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;              else if(j<0){
   int *popage;                nberr++;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;                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]);
   double *popeffectif,*popcount;                j=1; /* Temporary Dangerous patch */
   double ***p3mat;                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);
   char fileresf[FILENAMELENGTH];                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
  agelim=AGESUP;              }
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;              k=k+1;
               if (j >= jmax){
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                jmax=j;
                  ijmax=i;
                }
   strcpy(fileresf,"f");              if (j <= jmin){
   strcat(fileresf,fileres);                jmin=j;
   if((ficresf=fopen(fileresf,"w"))==NULL) {                ijmin=i;
     printf("Problem with forecast resultfile: %s\n", fileresf);              }
   }              sum=sum+j;
   printf("Computing forecasting: result on file '%s' \n", fileresf);              /*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);*/
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            }
           }
   if (mobilav==1) {          else{
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     movingaverage(agedeb, fage, ageminpar, mobaverage);  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
   }  
             k=k+1;
   stepsize=(int) (stepm+YEARM-1)/YEARM;            if (j >= jmax) {
   if (stepm<=12) stepsize=1;              jmax=j;
                ijmax=i;
   agelim=AGESUP;            }
              else if (j <= jmin){
   hstepm=1;              jmin=j;
   hstepm=hstepm/stepm;              ijmin=i;
   yp1=modf(dateintmean,&yp);            }
   anprojmean=yp;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   yp2=modf((yp1*12),&yp);            /*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]);*/
   mprojmean=yp;            if(j<0){
   yp1=modf((yp2*30.5),&yp);              nberr++;
   jprojmean=yp;              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]);
   if(jprojmean==0) jprojmean=1;              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   if(mprojmean==0) jprojmean=1;            }
              sum=sum+j;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);          }
            jk= j/stepm;
   for(cptcov=1;cptcov<=i2;cptcov++){          jl= j -jk*stepm;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          ju= j -(jk+1)*stepm;
       k=k+1;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       fprintf(ficresf,"\n#******");            if(jl==0){
       for(j=1;j<=cptcoveff;j++) {              dh[mi][i]=jk;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              bh[mi][i]=0;
       }            }else{ /* We want a negative bias in order to only have interpolation ie
       fprintf(ficresf,"******\n");                    * at the price of an extra matrix product in likelihood */
       fprintf(ficresf,"# StartingAge FinalAge");              dh[mi][i]=jk+1;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);              bh[mi][i]=ju;
                  }
                }else{
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {            if(jl <= -ju){
         fprintf(ficresf,"\n");              dh[mi][i]=jk;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);                bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){                                   */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            }
           nhstepm = nhstepm/hstepm;            else{
                        dh[mi][i]=jk+1;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              bh[mi][i]=ju;
           oldm=oldms;savm=savms;            }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              if(dh[mi][i]==0){
                      dh[mi][i]=1; /* At least one step */
           for (h=0; h<=nhstepm; h++){              bh[mi][i]=ju; /* At least one step */
             if (h==(int) (calagedate+YEARM*cpt)) {              /*  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(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);            }
             }          } /* end if mle */
             for(j=1; j<=nlstate+ndeath;j++) {        }
               kk1=0.;kk2=0;      } /* end wave */
               for(i=1; i<=nlstate;i++) {                  }
                 if (mobilav==1)    jmean=sum/k;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    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);
                 else {    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);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];   }
                 }  
                  /*********** Tricode ****************************/
               }  void tricode(int *Tvar, int **nbcode, int imx)
               if (h==(int)(calagedate+12*cpt)){  {
                 fprintf(ficresf," %.3f", kk1);    
                            int Ndum[20],ij=1, k, j, i, maxncov=19;
               }    int cptcode=0;
             }    cptcoveff=0; 
           }   
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (k=0; k<maxncov; k++) Ndum[k]=0;
         }    for (k=1; k<=7; k++) ncodemax[k]=0;
       }  
     }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                         modality*/ 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         Ndum[ij]++; /*store the modality */
   fclose(ficresf);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
 }        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
 /************** Forecasting ******************/                                         Tvar[j]. If V=sex and male is 0 and 
 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){                                         female is 1, then  cptcode=1.*/
        }
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  
   int *popage;      for (i=0; i<=cptcode; i++) {
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        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 */
   double *popeffectif,*popcount;      }
   double ***p3mat,***tabpop,***tabpopprev;  
   char filerespop[FILENAMELENGTH];      ij=1; 
       for (i=1; i<=ncodemax[j]; i++) {
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for (k=0; k<= maxncov; k++) {
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          if (Ndum[k] != 0) {
   agelim=AGESUP;            nbcode[Tvar[j]][ij]=k; 
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;            /* 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; */
              
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            ij++;
            }
            if (ij > ncodemax[j]) break; 
   strcpy(filerespop,"pop");        }  
   strcat(filerespop,fileres);      } 
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    }  
     printf("Problem with forecast resultfile: %s\n", filerespop);  
   }   for (k=0; k< maxncov; k++) Ndum[k]=0;
   printf("Computing forecasting: result on file '%s' \n", filerespop);  
    for (i=1; i<=ncovmodel-2; i++) { 
   if (cptcoveff==0) ncodemax[cptcoveff]=1;     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
      ij=Tvar[i];
   if (mobilav==1) {     Ndum[ij]++;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   }
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }   ij=1;
    for (i=1; i<= maxncov; i++) {
   stepsize=(int) (stepm+YEARM-1)/YEARM;     if((Ndum[i]!=0) && (i<=ncovcol)){
   if (stepm<=12) stepsize=1;       Tvaraff[ij]=i; /*For printing */
         ij++;
   agelim=AGESUP;     }
     }
   hstepm=1;   
   hstepm=hstepm/stepm;   cptcoveff=ij-1; /*Number of simple covariates*/
    }
   if (popforecast==1) {  
     if((ficpop=fopen(popfile,"r"))==NULL) {  /*********** Health Expectancies ****************/
       printf("Problem with population file : %s\n",popfile);exit(0);  
     }  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);  {
     popcount=vector(0,AGESUP);    /* Health expectancies, no variances */
        int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
     i=1;      int nhstepma, nstepma; /* Decreasing with age */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    double age, agelim, hf;
        double ***p3mat;
     imx=i;    double eip;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];  
   }    pstamp(ficreseij);
     fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   for(cptcov=1;cptcov<=i2;cptcov++){    fprintf(ficreseij,"# Age");
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    for(i=1; i<=nlstate;i++){
       k=k+1;      for(j=1; j<=nlstate;j++){
       fprintf(ficrespop,"\n#******");        fprintf(ficreseij," e%1d%1d ",i,j);
       for(j=1;j<=cptcoveff;j++) {      }
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficreseij," e%1d. ",i);
       }    }
       fprintf(ficrespop,"******\n");    fprintf(ficreseij,"\n");
       fprintf(ficrespop,"# Age");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    
       if (popforecast==1)  fprintf(ficrespop," [Population]");    if(estepm < stepm){
            printf ("Problem %d lower than %d\n",estepm, stepm);
       for (cpt=0; cpt<=0;cpt++) {    }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      else  hstepm=estepm;   
            /* We compute the life expectancy from trapezoids spaced every estepm months
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){     * This is mainly to measure the difference between two models: for example
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);     * if stepm=24 months pijx are given only every 2 years and by summing them
           nhstepm = nhstepm/hstepm;     * we are calculating an estimate of the Life Expectancy assuming a linear 
               * progression in between and thus overestimating or underestimating according
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     * to the curvature of the survival function. If, for the same date, we 
           oldm=oldms;savm=savms;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       * to compare the new estimate of Life expectancy with the same linear 
             * hypothesis. A more precise result, taking into account a more precise
           for (h=0; h<=nhstepm; h++){     * curvature will be obtained if estepm is as small as stepm. */
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    /* 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(j=1; j<=nlstate+ndeath;j++) {       nhstepm is the number of hstepm from age to agelim 
               kk1=0.;kk2=0;       nstepm is the number of stepm from age to agelin. 
               for(i=1; i<=nlstate;i++) {                     Look at hpijx to understand the reason of that which relies in memory size
                 if (mobilav==1)       and note for a fixed period like estepm months */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                 else {       survival function given by stepm (the optimization length). Unfortunately it
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];       means that if the survival funtion is printed only each two years of age and if
                 }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
               }       results. So we changed our mind and took the option of the best precision.
               if (h==(int)(calagedate+12*cpt)){    */
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                   /*fprintf(ficrespop," %.3f", kk1);  
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    agelim=AGESUP;
               }    /* If stepm=6 months */
             }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
             for(i=1; i<=nlstate;i++){         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
               kk1=0.;      
                 for(j=1; j<=nlstate;j++){  /* nhstepm age range expressed in number of stepm */
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
                 }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    /* if (stepm >= YEARM) hstepm=1;*/
             }    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)  
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    for (age=bage; age<=fage; age ++){ 
           }      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      /* 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 */
    
   /******/      /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      
           nhstepm = nhstepm/hstepm;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
                
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      printf("%d|",(int)age);fflush(stdout);
           oldm=oldms;savm=savms;      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        
           for (h=0; h<=nhstepm; h++){      /* Computing expectancies */
             if (h==(int) (calagedate+YEARM*cpt)) {      for(i=1; i<=nlstate;i++)
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        for(j=1; j<=nlstate;j++)
             }          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             for(j=1; j<=nlstate+ndeath;j++) {            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
               kk1=0.;kk2=0;            
               for(i=1; i<=nlstate;i++) {                          /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      
               }          }
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  
             }      fprintf(ficreseij,"%3.0f",age );
           }      for(i=1; i<=nlstate;i++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        eip=0;
         }        for(j=1; j<=nlstate;j++){
       }          eip +=eij[i][j][(int)age];
    }          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   }        }
          fprintf(ficreseij,"%9.4f", eip );
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      }
       fprintf(ficreseij,"\n");
   if (popforecast==1) {      
     free_ivector(popage,0,AGESUP);    }
     free_vector(popeffectif,0,AGESUP);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_vector(popcount,0,AGESUP);    printf("\n");
   }    fprintf(ficlog,"\n");
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  }
   fclose(ficrespop);  
 }  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[] )
   
 /***********************************************/  {
 /**************** Main Program *****************/    /* Covariances of health expectancies eij and of total life expectancies according
 /***********************************************/     to initial status i, ei. .
     */
 int main(int argc, char *argv[])    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
 {    int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    double ***p3matp, ***p3matm, ***varhe;
   double agedeb, agefin,hf;    double **dnewm,**doldm;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    double *xp, *xm;
     double **gp, **gm;
   double fret;    double ***gradg, ***trgradg;
   double **xi,tmp,delta;    int theta;
   
   double dum; /* Dummy variable */    double eip, vip;
   double ***p3mat;  
   int *indx;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   char line[MAXLINE], linepar[MAXLINE];    xp=vector(1,npar);
   char title[MAXLINE];    xm=vector(1,npar);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    dnewm=matrix(1,nlstate*nlstate,1,npar);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
      
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    pstamp(ficresstdeij);
     fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
   char filerest[FILENAMELENGTH];    fprintf(ficresstdeij,"# Age");
   char fileregp[FILENAMELENGTH];    for(i=1; i<=nlstate;i++){
   char popfile[FILENAMELENGTH];      for(j=1; j<=nlstate;j++)
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
   int firstobs=1, lastobs=10;      fprintf(ficresstdeij," e%1d. ",i);
   int sdeb, sfin; /* Status at beginning and end */    }
   int c,  h , cpt,l;    fprintf(ficresstdeij,"\n");
   int ju,jl, mi;  
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    pstamp(ficrescveij);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   int mobilav=0,popforecast=0;    fprintf(ficrescveij,"# Age");
   int hstepm, nhstepm;    for(i=1; i<=nlstate;i++)
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;      for(j=1; j<=nlstate;j++){
         cptj= (j-1)*nlstate+i;
   double bage, fage, age, agelim, agebase;        for(i2=1; i2<=nlstate;i2++)
   double ftolpl=FTOL;          for(j2=1; j2<=nlstate;j2++){
   double **prlim;            cptj2= (j2-1)*nlstate+i2;
   double *severity;            if(cptj2 <= cptj)
   double ***param; /* Matrix of parameters */              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
   double  *p;          }
   double **matcov; /* Matrix of covariance */      }
   double ***delti3; /* Scale */    fprintf(ficrescveij,"\n");
   double *delti; /* Scale */    
   double ***eij, ***vareij;    if(estepm < stepm){
   double **varpl; /* Variances of prevalence limits by age */      printf ("Problem %d lower than %d\n",estepm, stepm);
   double *epj, vepp;    }
   double kk1, kk2;    else  hstepm=estepm;   
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    /* We compute the life expectancy from trapezoids spaced every estepm months
       * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
   char version[80]="Imach version 0.8a, May 2002, INED-EUROREVES ";     * we are calculating an estimate of the Life Expectancy assuming a linear 
   char *alph[]={"a","a","b","c","d","e"}, str[4];     * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
   char z[1]="c", occ;     * to compare the new estimate of Life expectancy with the same linear 
 #include <sys/time.h>     * hypothesis. A more precise result, taking into account a more precise
 #include <time.h>     * curvature will be obtained if estepm is as small as stepm. */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  
      /* For example we decided to compute the life expectancy with the smallest unit */
   /* long total_usecs;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   struct timeval start_time, end_time;       nhstepm is the number of hstepm from age to agelim 
         nstepm is the number of stepm from age to agelin. 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */       Look at hpijx to understand the reason of that which relies in memory size
   getcwd(pathcd, size);       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   printf("\n%s",version);       survival function given by stepm (the optimization length). Unfortunately it
   if(argc <=1){       means that if the survival funtion is printed only each two years of age and if
     printf("\nEnter the parameter file name: ");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     scanf("%s",pathtot);       results. So we changed our mind and took the option of the best precision.
   }    */
   else{    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     strcpy(pathtot,argv[1]);  
   }    /* If stepm=6 months */
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    /* nhstepm age range expressed in number of stepm */
   /*cygwin_split_path(pathtot,path,optionfile);    agelim=AGESUP;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
   /* cutv(path,optionfile,pathtot,'\\');*/    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    
   chdir(path);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   replace(pathc,path);    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
 /*-------- arguments in the command line --------*/    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     gp=matrix(0,nhstepm,1,nlstate*nlstate);
   strcpy(fileres,"r");    gm=matrix(0,nhstepm,1,nlstate*nlstate);
   strcat(fileres, optionfilefiname);  
   strcat(fileres,".txt");    /* Other files have txt extension */    for (age=bage; age<=fage; age ++){ 
       nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   /*---------arguments file --------*/      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     printf("Problem with optionfile %s\n",optionfile);  
     goto end;      /* 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 */
   strcpy(filereso,"o");      
   strcat(filereso,fileres);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   if((ficparo=fopen(filereso,"w"))==NULL) {  
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      /* Computing  Variances of health expectancies */
   }      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
   /* Reads comments: lines beginning with '#' */      for(theta=1; theta <=npar; theta++){
   while((c=getc(ficpar))=='#' && c!= EOF){        for(i=1; i<=npar; i++){ 
     ungetc(c,ficpar);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     fgets(line, MAXLINE, ficpar);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
     puts(line);        }
     fputs(line,ficparo);        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
   }        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
   ungetc(c,ficpar);    
         for(j=1; j<= nlstate; j++){
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);          for(i=1; i<=nlstate; i++){
   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);            for(h=0; h<=nhstepm-1; h++){
   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);              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
 while((c=getc(ficpar))=='#' && c!= EOF){              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
     ungetc(c,ficpar);            }
     fgets(line, MAXLINE, ficpar);          }
     puts(line);        }
     fputs(line,ficparo);       
   }        for(ij=1; ij<= nlstate*nlstate; ij++)
   ungetc(c,ficpar);          for(h=0; h<=nhstepm-1; h++){
              gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
              }
   covar=matrix(0,NCOVMAX,1,n);      }/* End theta */
   cptcovn=0;      
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      
       for(h=0; h<=nhstepm-1; h++)
   ncovmodel=2+cptcovn;        for(j=1; j<=nlstate*nlstate;j++)
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */          for(theta=1; theta <=npar; theta++)
              trgradg[h][j][theta]=gradg[h][theta][j];
   /* Read guess parameters */      
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){       for(ij=1;ij<=nlstate*nlstate;ij++)
     ungetc(c,ficpar);        for(ji=1;ji<=nlstate*nlstate;ji++)
     fgets(line, MAXLINE, ficpar);          varhe[ij][ji][(int)age] =0.;
     puts(line);  
     fputs(line,ficparo);       printf("%d|",(int)age);fflush(stdout);
   }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   ungetc(c,ficpar);       for(h=0;h<=nhstepm-1;h++){
          for(k=0;k<=nhstepm-1;k++){
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     for(i=1; i <=nlstate; i++)          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     for(j=1; j <=nlstate+ndeath-1; j++){          for(ij=1;ij<=nlstate*nlstate;ij++)
       fscanf(ficpar,"%1d%1d",&i1,&j1);            for(ji=1;ji<=nlstate*nlstate;ji++)
       fprintf(ficparo,"%1d%1d",i1,j1);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
       printf("%1d%1d",i,j);        }
       for(k=1; k<=ncovmodel;k++){      }
         fscanf(ficpar," %lf",&param[i][j][k]);  
         printf(" %lf",param[i][j][k]);      /* Computing expectancies */
         fprintf(ficparo," %lf",param[i][j][k]);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       }      for(i=1; i<=nlstate;i++)
       fscanf(ficpar,"\n");        for(j=1; j<=nlstate;j++)
       printf("\n");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       fprintf(ficparo,"\n");            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
     }            
              /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  
           }
   p=param[1][1];  
        fprintf(ficresstdeij,"%3.0f",age );
   /* Reads comments: lines beginning with '#' */      for(i=1; i<=nlstate;i++){
   while((c=getc(ficpar))=='#' && c!= EOF){        eip=0.;
     ungetc(c,ficpar);        vip=0.;
     fgets(line, MAXLINE, ficpar);        for(j=1; j<=nlstate;j++){
     puts(line);          eip += eij[i][j][(int)age];
     fputs(line,ficparo);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
   }            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
   ungetc(c,ficpar);          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      }
   for(i=1; i <=nlstate; i++){      fprintf(ficresstdeij,"\n");
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);      fprintf(ficrescveij,"%3.0f",age );
       printf("%1d%1d",i,j);      for(i=1; i<=nlstate;i++)
       fprintf(ficparo,"%1d%1d",i1,j1);        for(j=1; j<=nlstate;j++){
       for(k=1; k<=ncovmodel;k++){          cptj= (j-1)*nlstate+i;
         fscanf(ficpar,"%le",&delti3[i][j][k]);          for(i2=1; i2<=nlstate;i2++)
         printf(" %le",delti3[i][j][k]);            for(j2=1; j2<=nlstate;j2++){
         fprintf(ficparo," %le",delti3[i][j][k]);              cptj2= (j2-1)*nlstate+i2;
       }              if(cptj2 <= cptj)
       fscanf(ficpar,"\n");                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
       printf("\n");            }
       fprintf(ficparo,"\n");        }
     }      fprintf(ficrescveij,"\n");
   }     
   delti=delti3[1][1];    }
      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   /* Reads comments: lines beginning with '#' */    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   while((c=getc(ficpar))=='#' && c!= EOF){    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     ungetc(c,ficpar);    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     fgets(line, MAXLINE, ficpar);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     puts(line);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fputs(line,ficparo);    printf("\n");
   }    fprintf(ficlog,"\n");
   ungetc(c,ficpar);  
      free_vector(xm,1,npar);
   matcov=matrix(1,npar,1,npar);    free_vector(xp,1,npar);
   for(i=1; i <=npar; i++){    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     fscanf(ficpar,"%s",&str);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     printf("%s",str);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     fprintf(ficparo,"%s",str);  }
     for(j=1; j <=i; j++){  
       fscanf(ficpar," %le",&matcov[i][j]);  /************ Variance ******************/
       printf(" %.5le",matcov[i][j]);  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
       fprintf(ficparo," %.5le",matcov[i][j]);  {
     }    /* Variance of health expectancies */
     fscanf(ficpar,"\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     printf("\n");    /* double **newm;*/
     fprintf(ficparo,"\n");    double **dnewm,**doldm;
   }    double **dnewmp,**doldmp;
   for(i=1; i <=npar; i++)    int i, j, nhstepm, hstepm, h, nstepm ;
     for(j=i+1;j<=npar;j++)    int k, cptcode;
       matcov[i][j]=matcov[j][i];    double *xp;
        double **gp, **gm;  /* for var eij */
   printf("\n");    double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     /*-------- Rewriting paramater file ----------*/    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
      strcpy(rfileres,"r");    /* "Rparameterfile */    double ***p3mat;
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    double age,agelim, hf;
      strcat(rfileres,".");    /* */    double ***mobaverage;
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    int theta;
     if((ficres =fopen(rfileres,"w"))==NULL) {    char digit[4];
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    char digitp[25];
     }  
     fprintf(ficres,"#%s\n",version);    char fileresprobmorprev[FILENAMELENGTH];
      
     /*-------- data file ----------*/    if(popbased==1){
     if((fic=fopen(datafile,"r"))==NULL)    {      if(mobilav!=0)
       printf("Problem with datafile: %s\n", datafile);goto end;        strcpy(digitp,"-populbased-mobilav-");
     }      else strcpy(digitp,"-populbased-nomobil-");
     }
     n= lastobs;    else 
     severity = vector(1,maxwav);      strcpy(digitp,"-stablbased-");
     outcome=imatrix(1,maxwav+1,1,n);  
     num=ivector(1,n);    if (mobilav!=0) {
     moisnais=vector(1,n);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     annais=vector(1,n);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     moisdc=vector(1,n);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     andc=vector(1,n);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     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 */    strcpy(fileresprobmorprev,"prmorprev"); 
     mint=matrix(1,maxwav,1,n);    sprintf(digit,"%-d",ij);
     anint=matrix(1,maxwav,1,n);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     s=imatrix(1,maxwav+1,1,n);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     adl=imatrix(1,maxwav+1,1,n);        strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     tab=ivector(1,NCOVMAX);    strcat(fileresprobmorprev,fileres);
     ncodemax=ivector(1,8);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
     i=1;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     while (fgets(line, MAXLINE, fic) != NULL)    {    }
       if ((i >= firstobs) && (i <=lastobs)) {    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           
         for (j=maxwav;j>=1;j--){    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    pstamp(ficresprobmorprev);
           strcpy(line,stra);    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);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         }      fprintf(ficresprobmorprev," p.%-d SE",j);
              for(i=1; i<=nlstate;i++)
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    }  
     fprintf(ficresprobmorprev,"\n");
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficgp,"\n# Routine varevsij");
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    /* 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");
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
         for (j=ncovcol;j>=1;j--){  /*   } */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         }    pstamp(ficresvij);
         num[i]=atol(stra);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
            if(popbased==1)
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
           printf("%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;}*/    else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
         i=i+1;    fprintf(ficresvij,"# Age");
       }    for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=nlstate;j++)
     /* printf("ii=%d", ij);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
        scanf("%d",i);*/    fprintf(ficresvij,"\n");
   imx=i-1; /* Number of individuals */  
     xp=vector(1,npar);
   /* for (i=1; i<=imx; i++){    dnewm=matrix(1,nlstate,1,npar);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    doldm=matrix(1,nlstate,1,nlstate);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     }*/  
    /*  for (i=1; i<=imx; i++){    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
      if (s[4][i]==9)  s[4][i]=-1;    gpp=vector(nlstate+1,nlstate+ndeath);
      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]));}*/    gmp=vector(nlstate+1,nlstate+ndeath);
      trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      
   /* Calculation of the number of parameter from char model*/    if(estepm < stepm){
   Tvar=ivector(1,15);      printf ("Problem %d lower than %d\n",estepm, stepm);
   Tprod=ivector(1,15);    }
   Tvaraff=ivector(1,15);    else  hstepm=estepm;   
   Tvard=imatrix(1,15,1,2);    /* For example we decided to compute the life expectancy with the smallest unit */
   Tage=ivector(1,15);          /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           nhstepm is the number of hstepm from age to agelim 
   if (strlen(model) >1){       nstepm is the number of stepm from age to agelin. 
     j=0, j1=0, k1=1, k2=1;       Look at function hpijx to understand why (it is linked to memory size questions) */
     j=nbocc(model,'+');    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     j1=nbocc(model,'*');       survival function given by stepm (the optimization length). Unfortunately it
     cptcovn=j+1;       means that if the survival funtion is printed every two years of age and if
     cptcovprod=j1;       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.
     strcpy(modelsav,model);    */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       printf("Error. Non available option model=%s ",model);    agelim = AGESUP;
       goto end;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     }      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
          nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     for(i=(j+1); i>=1;i--){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       cutv(stra,strb,modelsav,'+');      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      gp=matrix(0,nhstepm,1,nlstate);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      gm=matrix(0,nhstepm,1,nlstate);
       /*scanf("%d",i);*/  
       if (strchr(strb,'*')) {  
         cutv(strd,strc,strb,'*');      for(theta=1; theta <=npar; theta++){
         if (strcmp(strc,"age")==0) {        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           cptcovprod--;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           cutv(strb,stre,strd,'V');        }
           Tvar[i]=atoi(stre);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           cptcovage++;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/        if (popbased==1) {
         }          if(mobilav ==0){
         else if (strcmp(strd,"age")==0) {            for(i=1; i<=nlstate;i++)
           cptcovprod--;              prlim[i][i]=probs[(int)age][i][ij];
           cutv(strb,stre,strc,'V');          }else{ /* mobilav */ 
           Tvar[i]=atoi(stre);            for(i=1; i<=nlstate;i++)
           cptcovage++;              prlim[i][i]=mobaverage[(int)age][i][ij];
           Tage[cptcovage]=i;          }
         }        }
         else {    
           cutv(strb,stre,strc,'V');        for(j=1; j<= nlstate; j++){
           Tvar[i]=ncovcol+k1;          for(h=0; h<=nhstepm; h++){
           cutv(strb,strc,strd,'V');            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
           Tprod[k1]=i;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           Tvard[k1][1]=atoi(strc);          }
           Tvard[k1][2]=atoi(stre);        }
           Tvar[cptcovn+k2]=Tvard[k1][1];        /* This for computing probability of death (h=1 means
           Tvar[cptcovn+k2+1]=Tvard[k1][2];           computed over hstepm matrices product = hstepm*stepm months) 
           for (k=1; k<=lastobs;k++)           as a weighted average of prlim.
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        */
           k1++;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           k2=k2+2;          for(i=1,gpp[j]=0.; i<= nlstate; i++)
         }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
       }        }    
       else {        /* end probability of death */
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  
        /*  scanf("%d",i);*/        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
       cutv(strd,strc,strb,'V');          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       Tvar[i]=atoi(strc);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       strcpy(modelsav,stra);     
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);        if (popbased==1) {
         scanf("%d",i);*/          if(mobilav ==0){
     }            for(i=1; i<=nlstate;i++)
 }              prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);            for(i=1; i<=nlstate;i++)
   printf("cptcovprod=%d ", cptcovprod);              prlim[i][i]=mobaverage[(int)age][i][ij];
   scanf("%d ",i);*/          }
     fclose(fic);        }
   
     /*  if(mle==1){*/        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
     if (weightopt != 1) { /* Maximisation without weights*/          for(h=0; h<=nhstepm; h++){
       for(i=1;i<=n;i++) weight[i]=1.0;            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     }              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     /*-calculation of age at interview from date of interview and age at death -*/          }
     agev=matrix(1,maxwav,1,imx);        }
         /* This for computing probability of death (h=1 means
     for (i=1; i<=imx; i++) {           computed over hstepm matrices product = hstepm*stepm months) 
       for(m=2; (m<= maxwav); m++) {           as a weighted average of prlim.
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        */
          anint[m][i]=9999;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
          s[m][i]=-1;          for(i=1,gmp[j]=0.; i<= nlstate; i++)
        }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;        }    
       }        /* end probability of death */
     }  
         for(j=1; j<= nlstate; j++) /* vareij */
     for (i=1; i<=imx; i++)  {          for(h=0; h<=nhstepm; h++){
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       for(m=1; (m<= maxwav); m++){          }
         if(s[m][i] >0){  
           if (s[m][i] >= nlstate+1) {        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
             if(agedc[i]>0)          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
               if(moisdc[i]!=99 && andc[i]!=9999)        }
                 agev[m][i]=agedc[i];  
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      } /* End theta */
            else {  
               if (andc[i]!=9999){      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;      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];
           else if(s[m][i] !=9){ /* Should no more exist */  
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
             if(mint[m][i]==99 || anint[m][i]==9999)        for(theta=1; theta <=npar; theta++)
               agev[m][i]=1;          trgradgp[j][theta]=gradgp[theta][j];
             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);*/      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
             }      for(i=1;i<=nlstate;i++)
             else if(agev[m][i] >agemax){        for(j=1;j<=nlstate;j++)
               agemax=agev[m][i];          vareij[i][j][(int)age] =0.;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  
             }      for(h=0;h<=nhstepm;h++){
             /*agev[m][i]=anint[m][i]-annais[i];*/        for(k=0;k<=nhstepm;k++){
             /*   agev[m][i] = age[i]+2*m;*/          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           }          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           else { /* =9 */          for(i=1;i<=nlstate;i++)
             agev[m][i]=1;            for(j=1;j<=nlstate;j++)
             s[m][i]=-1;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
           }        }
         }      }
         else /*= 0 Unknown */    
           agev[m][i]=1;      /* pptj */
       }      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
          matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     }      for(j=nlstate+1;j<=nlstate+ndeath;j++)
     for (i=1; i<=imx; i++)  {        for(i=nlstate+1;i<=nlstate+ndeath;i++)
       for(m=1; (m<= maxwav); m++){          varppt[j][i]=doldmp[j][i];
         if (s[m][i] > (nlstate+ndeath)) {      /* end ppptj */
           printf("Error: Wrong value in nlstate or ndeath\n");        /*  x centered again */
           goto end;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
         }      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
       }   
     }      if (popbased==1) {
         if(mobilav ==0){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
     free_vector(severity,1,maxwav);        }else{ /* mobilav */ 
     free_imatrix(outcome,1,maxwav+1,1,n);          for(i=1; i<=nlstate;i++)
     free_vector(moisnais,1,n);            prlim[i][i]=mobaverage[(int)age][i][ij];
     free_vector(annais,1,n);        }
     /* free_matrix(mint,1,maxwav,1,n);      }
        free_matrix(anint,1,maxwav,1,n);*/               
     free_vector(moisdc,1,n);      /* This for computing probability of death (h=1 means
     free_vector(andc,1,n);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
          */
     wav=ivector(1,imx);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
          }    
     /* Concatenates waves */      /* end probability of death */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       Tcode=ivector(1,100);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        for(i=1; i<=nlstate;i++){
       ncodemax[1]=1;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        }
            } 
    codtab=imatrix(1,100,1,10);      fprintf(ficresprobmorprev,"\n");
    h=0;  
    m=pow(2,cptcoveff);      fprintf(ficresvij,"%.0f ",age );
        for(i=1; i<=nlstate;i++)
    for(k=1;k<=cptcoveff; k++){        for(j=1; j<=nlstate;j++){
      for(i=1; i <=(m/pow(2,k));i++){          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
        for(j=1; j <= ncodemax[k]; j++){        }
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      fprintf(ficresvij,"\n");
            h++;      free_matrix(gp,0,nhstepm,1,nlstate);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;      free_matrix(gm,0,nhstepm,1,nlstate);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
          }      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
        }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      }    } /* End age */
    }    free_vector(gpp,nlstate+1,nlstate+ndeath);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    free_vector(gmp,nlstate+1,nlstate+ndeath);
       codtab[1][2]=1;codtab[2][2]=2; */    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
    /* for(i=1; i <=m ;i++){    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       for(k=1; k <=cptcovn; k++){    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       }    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       printf("\n");  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
       }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
       scanf("%d",i);*/  /*   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));
    /* Calculates basic frequencies. Computes observed prevalence at single age    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
        and prints on file fileres'p'. */    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
        fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
        /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    free_vector(xp,1,npar);
          free_matrix(doldm,1,nlstate,1,nlstate);
     /* For Powell, parameters are in a vector p[] starting at p[1]    free_matrix(dnewm,1,nlstate,1,npar);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if(mle==1){    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    fclose(ficresprobmorprev);
     }    fflush(ficgp);
        fflush(fichtm); 
     /*--------- results files --------------*/  }  /* end varevsij */
     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);  
    /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
    jk=1;  {
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    /* Variance of prevalence limit */
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
    for(i=1,jk=1; i <=nlstate; i++){    double **newm;
      for(k=1; k <=(nlstate+ndeath); k++){    double **dnewm,**doldm;
        if (k != i)    int i, j, nhstepm, hstepm;
          {    int k, cptcode;
            printf("%d%d ",i,k);    double *xp;
            fprintf(ficres,"%1d%1d ",i,k);    double *gp, *gm;
            for(j=1; j <=ncovmodel; j++){    double **gradg, **trgradg;
              printf("%f ",p[jk]);    double age,agelim;
              fprintf(ficres,"%f ",p[jk]);    int theta;
              jk++;    
            }    pstamp(ficresvpl);
            printf("\n");    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
            fprintf(ficres,"\n");    fprintf(ficresvpl,"# Age");
          }    for(i=1; i<=nlstate;i++)
      }        fprintf(ficresvpl," %1d-%1d",i,i);
    }    fprintf(ficresvpl,"\n");
  if(mle==1){  
     /* Computing hessian and covariance matrix */    xp=vector(1,npar);
     ftolhess=ftol; /* Usually correct */    dnewm=matrix(1,nlstate,1,npar);
     hesscov(matcov, p, npar, delti, ftolhess, func);    doldm=matrix(1,nlstate,1,nlstate);
  }    
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    hstepm=1*YEARM; /* Every year of age */
     printf("# Scales (for hessian or gradient estimation)\n");    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
      for(i=1,jk=1; i <=nlstate; i++){    agelim = AGESUP;
       for(j=1; j <=nlstate+ndeath; j++){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         if (j!=i) {      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           fprintf(ficres,"%1d%1d",i,j);      if (stepm >= YEARM) hstepm=1;
           printf("%1d%1d",i,j);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           for(k=1; k<=ncovmodel;k++){      gradg=matrix(1,npar,1,nlstate);
             printf(" %.5e",delti[jk]);      gp=vector(1,nlstate);
             fprintf(ficres," %.5e",delti[jk]);      gm=vector(1,nlstate);
             jk++;  
           }      for(theta=1; theta <=npar; theta++){
           printf("\n");        for(i=1; i<=npar; i++){ /* Computes gradient */
           fprintf(ficres,"\n");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }        }
       }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      }        for(i=1;i<=nlstate;i++)
              gp[i] = prlim[i][i];
     k=1;      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");        for(i=1; i<=npar; i++) /* Computes gradient */
     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");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     for(i=1;i<=npar;i++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       /*  if (k>nlstate) k=1;        for(i=1;i<=nlstate;i++)
       i1=(i-1)/(ncovmodel*nlstate)+1;          gm[i] = prlim[i][i];
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  
       printf("%s%d%d",alph[k],i1,tab[i]);*/        for(i=1;i<=nlstate;i++)
       fprintf(ficres,"%3d",i);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       printf("%3d",i);      } /* End theta */
       for(j=1; j<=i;j++){  
         fprintf(ficres," %.5e",matcov[i][j]);      trgradg =matrix(1,nlstate,1,npar);
         printf(" %.5e",matcov[i][j]);  
       }      for(j=1; j<=nlstate;j++)
       fprintf(ficres,"\n");        for(theta=1; theta <=npar; theta++)
       printf("\n");          trgradg[j][theta]=gradg[theta][j];
       k++;  
     }      for(i=1;i<=nlstate;i++)
            varpl[i][(int)age] =0.;
     while((c=getc(ficpar))=='#' && c!= EOF){      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       ungetc(c,ficpar);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       fgets(line, MAXLINE, ficpar);      for(i=1;i<=nlstate;i++)
       puts(line);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
       fputs(line,ficparo);  
     }      fprintf(ficresvpl,"%.0f ",age );
     ungetc(c,ficpar);      for(i=1; i<=nlstate;i++)
     estepm=0;        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);      fprintf(ficresvpl,"\n");
     if (estepm==0 || estepm < stepm) estepm=stepm;      free_vector(gp,1,nlstate);
     if (fage <= 2) {      free_vector(gm,1,nlstate);
       bage = ageminpar;      free_matrix(gradg,1,npar,1,nlstate);
       fage = agemaxpar;      free_matrix(trgradg,1,nlstate,1,npar);
     }    } /* End age */
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    free_vector(xp,1,npar);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    free_matrix(doldm,1,nlstate,1,npar);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    free_matrix(dnewm,1,nlstate,1,nlstate);
    
     while((c=getc(ficpar))=='#' && c!= EOF){  }
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  /************ Variance of one-step probabilities  ******************/
     puts(line);  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[])
     fputs(line,ficparo);  {
   }    int i, j=0,  i1, k1, l1, t, tj;
   ungetc(c,ficpar);    int k2, l2, j1,  z1;
      int k=0,l, cptcode;
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    int first=1, first1;
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    double **dnewm,**doldm;
          double *xp;
   while((c=getc(ficpar))=='#' && c!= EOF){    double *gp, *gm;
     ungetc(c,ficpar);    double **gradg, **trgradg;
     fgets(line, MAXLINE, ficpar);    double **mu;
     puts(line);    double age,agelim, cov[NCOVMAX];
     fputs(line,ficparo);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   }    int theta;
   ungetc(c,ficpar);    char fileresprob[FILENAMELENGTH];
      char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
    dateprev1=anprev1+mprev1/12.+jprev1/365.;  
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    double ***varpij;
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);    strcpy(fileresprob,"prob"); 
   fprintf(ficparo,"pop_based=%d\n",popbased);      strcat(fileresprob,fileres);
   fprintf(ficres,"pop_based=%d\n",popbased);      if((ficresprob=fopen(fileresprob,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprob);
   while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    strcpy(fileresprobcov,"probcov"); 
     puts(line);    strcat(fileresprobcov,fileres);
     fputs(line,ficparo);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprobcov);
   ungetc(c,ficpar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);    strcpy(fileresprobcor,"probcor"); 
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    strcat(fileresprobcor,fileres);
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
 while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fgets(line, MAXLINE, ficpar);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     puts(line);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fputs(line,ficparo);    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);
   ungetc(c,ficpar);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    fprintf(ficresprob,"# Age");
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
 /*------------ gnuplot -------------*/    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);    fprintf(ficresprobcor,"# Age");
    
 /*------------ free_vector  -------------*/  
  chdir(path);    for(i=1; i<=nlstate;i++)
        for(j=1; j<=(nlstate+ndeath);j++){
  free_ivector(wav,1,imx);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          fprintf(ficresprobcor," p%1d-%1d ",i,j);
  free_ivector(num,1,n);      }  
  free_vector(agedc,1,n);   /* fprintf(ficresprob,"\n");
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    fprintf(ficresprobcov,"\n");
  fclose(ficparo);    fprintf(ficresprobcor,"\n");
  fclose(ficres);   */
    xp=vector(1,npar);
 /*--------- index.htm --------*/    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);    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;
   /*--------------- Prevalence limit --------------*/    fprintf(ficgp,"\n# Routine varprob");
      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   strcpy(filerespl,"pl");    fprintf(fichtm,"\n");
   strcat(filerespl,fileres);  
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
   }    file %s<br>\n",optionfilehtmcov);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   fprintf(ficrespl,"#Prevalence limit\n");  and drawn. It helps understanding how is the covariance between two incidences.\
   fprintf(ficrespl,"#Age ");   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    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. \
   fprintf(ficrespl,"\n");  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 \
   prlim=matrix(1,nlstate,1,nlstate);  standard deviations wide on each axis. <br>\
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    cov[1]=1;
   k=0;    tj=cptcoveff;
   agebase=ageminpar;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   agelim=agemaxpar;    j1=0;
   ftolpl=1.e-10;    for(t=1; t<=tj;t++){
   i1=cptcoveff;      for(i1=1; i1<=ncodemax[t];i1++){ 
   if (cptcovn < 1){i1=1;}        j1++;
         if  (cptcovn>0) {
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(ficresprob, "\n#********** Variable "); 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         k=k+1;          fprintf(ficresprob, "**********\n#\n");
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          fprintf(ficresprobcov, "\n#********** Variable "); 
         fprintf(ficrespl,"\n#******");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         for(j=1;j<=cptcoveff;j++)          fprintf(ficresprobcov, "**********\n#\n");
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          
         fprintf(ficrespl,"******\n");          fprintf(ficgp, "\n#********** Variable "); 
                  for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         for (age=agebase; age<=agelim; age++){          fprintf(ficgp, "**********\n#\n");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          
           fprintf(ficrespl,"%.0f",age );          
           for(i=1; i<=nlstate;i++)          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           fprintf(ficrespl," %.5f", prlim[i][i]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficrespl,"\n");          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]]);
   fclose(ficrespl);          fprintf(ficresprobcor, "**********\n#");    
         }
   /*------------- h Pij x at various ages ------------*/        
          for (age=bage; age<=fage; age ++){ 
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          cov[2]=age;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {          for (k=1; k<=cptcovn;k++) {
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   }          }
   printf("Computing pij: result on file '%s' \n", filerespij);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
            for (k=1; k<=cptcovprod;k++)
   stepsize=(int) (stepm+YEARM-1)/YEARM;            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   /*if (stepm<=24) stepsize=2;*/          
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   agelim=AGESUP;          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   hstepm=stepsize*YEARM; /* Every year of age */          gp=vector(1,(nlstate)*(nlstate+ndeath));
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          gm=vector(1,(nlstate)*(nlstate+ndeath));
        
   k=0;          for(theta=1; theta <=npar; theta++){
   for(cptcov=1;cptcov<=i1;cptcov++){            for(i=1; i<=npar; i++)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       k=k+1;            
         fprintf(ficrespij,"\n#****** ");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
         for(j=1;j<=cptcoveff;j++)            
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            k=0;
         fprintf(ficrespij,"******\n");            for(i=1; i<= (nlstate); i++){
                      for(j=1; j<=(nlstate+ndeath);j++){
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                k=k+1;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                gp[k]=pmmij[i][j];
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              }
           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(i=1; i<=npar; i++)
           fprintf(ficrespij,"# Age");              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
           for(i=1; i<=nlstate;i++)      
             for(j=1; j<=nlstate+ndeath;j++)            pmij(pmmij,cov,ncovmodel,xp,nlstate);
               fprintf(ficrespij," %1d-%1d",i,j);            k=0;
           fprintf(ficrespij,"\n");            for(i=1; i<=(nlstate); i++){
            for (h=0; h<=nhstepm; h++){              for(j=1; j<=(nlstate+ndeath);j++){
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );                k=k+1;
             for(i=1; i<=nlstate;i++)                gm[k]=pmmij[i][j];
               for(j=1; j<=nlstate+ndeath;j++)              }
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            }
             fprintf(ficrespij,"\n");       
              }            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           fprintf(ficrespij,"\n");          }
         }  
     }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   }            for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);          
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   fclose(ficrespij);          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));
   /*---------- Forecasting ------------------*/          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   if((stepm == 1) && (strcmp(model,".")==0)){          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);  
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);          pmij(pmmij,cov,ncovmodel,x,nlstate);
   }          
   else{          k=0;
     erreur=108;          for(i=1; i<=(nlstate); i++){
     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);            for(j=1; j<=(nlstate+ndeath);j++){
   }              k=k+1;
                mu[k][(int) age]=pmmij[i][j];
             }
   /*---------- Health expectancies and variances ------------*/          }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   strcpy(filerest,"t");            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   strcat(filerest,fileres);              varpij[i][j][(int)age] = doldm[i][j];
   if((ficrest=fopen(filerest,"w"))==NULL) {  
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;          /*printf("\n%d ",(int)age);
   }            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   printf("Computing Total LEs with variances: file '%s' \n", filerest);            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]));
             }*/
   strcpy(filerese,"e");  
   strcat(filerese,fileres);          fprintf(ficresprob,"\n%d ",(int)age);
   if((ficreseij=fopen(filerese,"w"))==NULL) {          fprintf(ficresprobcov,"\n%d ",(int)age);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          fprintf(ficresprobcor,"\n%d ",(int)age);
   }  
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
  strcpy(fileresv,"v");          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   strcat(fileresv,fileres);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          }
   }          i=0;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          for (k=1; k<=(nlstate);k++){
   calagedate=-1;            for (l=1; l<=(nlstate+ndeath);l++){ 
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   k=0;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   for(cptcov=1;cptcov<=i1;cptcov++){              for (j=1; j<=i;j++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
       k=k+1;                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
       fprintf(ficrest,"\n#****** ");              }
       for(j=1;j<=cptcoveff;j++)            }
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          }/* end of loop for state */
       fprintf(ficrest,"******\n");        } /* end of loop for age */
   
       fprintf(ficreseij,"\n#****** ");        /* Confidence intervalle of pij  */
       for(j=1;j<=cptcoveff;j++)        /*
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficgp,"\nset noparametric;unset label");
       fprintf(ficreseij,"******\n");          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(ficresvij,"\n#****** ");          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
       for(j=1;j<=cptcoveff;j++)          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       fprintf(ficresvij,"******\n");          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);          first1=1;
          for (k2=1; k2<=(nlstate);k2++){
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
       oldm=oldms;savm=savms;            if(l2==k2) continue;
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);            j=(k2-1)*(nlstate+ndeath)+l2;
                for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                  if(l1==k1) continue;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                i=(k1-1)*(nlstate+ndeath)+l1;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                if(i<=j) continue;
       fprintf(ficrest,"\n");                for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
       epj=vector(1,nlstate+1);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
       for(age=bage; age <=fage ;age++){                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
         if (popbased==1) {                    mu1=mu[i][(int) age]/stepm*YEARM ;
           for(i=1; i<=nlstate;i++)                    mu2=mu[j][(int) age]/stepm*YEARM;
             prlim[i][i]=probs[(int)age][i][k];                    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.;
         fprintf(ficrest," %4.0f",age);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                    /* Eigen vectors */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
             epj[j] += prlim[i][i]*eij[i][j][(int)age];                    /*v21=sqrt(1.-v11*v11); *//* error */
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/                    v21=(lc1-v1)/cv12*v11;
           }                    v12=-v21;
           epj[nlstate+1] +=epj[j];                    v22=v11;
         }                    tnalp=v21/v11;
                     if(first1==1){
         for(i=1, vepp=0.;i <=nlstate;i++)                      first1=0;
           for(j=1;j <=nlstate;j++)                      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);
             vepp += vareij[i][j][(int)age];                    }
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));                    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);
         for(j=1;j <=nlstate;j++){                    /*printf(fignu*/
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
         }                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
         fprintf(ficrest,"\n");                    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);
 free_matrix(mint,1,maxwav,1,n);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
     free_vector(weight,1,n);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   fclose(ficreseij);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
   fclose(ficresvij);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
   fclose(ficrest);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   fclose(ficpar);                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   free_vector(epj,1,nlstate+1);                      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);
   /*------- Variance limit prevalence------*/                        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);
   strcpy(fileresvpl,"vpl");                      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",\
   strcat(fileresvpl,fileres);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);                    }else{
     exit(0);                      first=0;
   }                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);                      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);
   k=0;                      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",\
   for(cptcov=1;cptcov<=i1;cptcov++){                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       k=k+1;                    }/* if first */
       fprintf(ficresvpl,"\n#****** ");                  } /* age mod 5 */
       for(j=1;j<=cptcoveff;j++)                } /* end loop age */
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
       fprintf(ficresvpl,"******\n");                first=1;
                    } /*l12 */
       varpl=matrix(1,nlstate,(int) bage, (int) fage);            } /* k12 */
       oldm=oldms;savm=savms;          } /*l1 */
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        }/* k1 */
     }      } /* loop covariates */
  }    }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   fclose(ficresvpl);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   /*---------- End : free ----------------*/    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    free_vector(xp,1,npar);
      fclose(ficresprob);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    fclose(ficresprobcov);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    fclose(ficresprobcor);
      fflush(ficgp);
      fflush(fichtmcov);
   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);  /******************* Printing html file ***********/
    void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   free_matrix(matcov,1,npar,1,npar);                    int lastpass, int stepm, int weightopt, char model[],\
   free_vector(delti,1,npar);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   free_matrix(agev,1,maxwav,1,imx);                    int popforecast, int estepm ,\
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                    double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
   if(erreur >0)    int jj1, k1, i1, cpt;
     printf("End of Imach with error or warning %d\n",erreur);  
   else   printf("End of Imach\n");     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
    </ul>");
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
   /*printf("Total time was %d uSec.\n", total_usecs);*/   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
   /*------ End -----------*/             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 ",
  end:             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
 #ifdef windows     fprintf(fichtm,"\
   /* chdir(pathcd);*/   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
 #endif             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
  /*system("wgnuplot graph.plt");*/     fprintf(fichtm,"\
  /*system("../gp37mgw/wgnuplot graph.plt");*/   - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
  /*system("cd ../gp37mgw");*/     <a href=\"%s\">%s</a> <br>\n",
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
  strcpy(plotcmd,GNUPLOTPROGRAM);     fprintf(fichtm,"\
  strcat(plotcmd," ");   - Population projections by age and states: \
  strcat(plotcmd,optionfilegnuplot);     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
  system(plotcmd);  
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
 #ifdef windows  
   while (z[0] != 'q') {   m=cptcoveff;
     /* chdir(path); */   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");  
     scanf("%s",z);   jj1=0;
     if (z[0] == 'c') system("./imach");   for(k1=1; k1<=m;k1++){
     else if (z[0] == 'e') system(optionfilehtm);     for(i1=1; i1<=ncodemax[k1];i1++){
     else if (z[0] == 'g') system(plotcmd);       jj1++;
     else if (z[0] == 'q') exit(0);       if (cptcovn > 0) {
   }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
 #endif         for (cpt=1; cpt<=cptcoveff;cpt++) 
 }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int 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;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char  *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     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);
           goto end;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* 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);
           pstamp(ficrest);
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms;
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
     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.1.41  
changed lines
  Added in v.1.129


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