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version 1.22, 2002/02/22 17:54:20 version 1.138, 2010/04/30 18:19:40
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 /* $Id$  /* $Id$
    Interpolate Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.138  2010/04/30 18:19:40  brouard
      *** empty log message ***
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.137  2010/04/29 18:11:38  brouard
   first survey ("cross") where individuals from different ages are    (Module): Checking covariates for more complex models
   interviewed on their health status or degree of disability (in the    than V1+V2. A lot of change to be done. Unstable.
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.136  2010/04/26 20:30:53  brouard
   (if any) in individual health status.  Health expectancies are    (Module): merging some libgsl code. Fixing computation
   computed from the time spent in each health state according to a    of likelione (using inter/intrapolation if mle = 0) in order to
   model. More health states you consider, more time is necessary to reach the    get same likelihood as if mle=1.
   Maximum Likelihood of the parameters involved in the model.  The    Some cleaning of code and comments added.
   simplest model is the multinomial logistic model where pij is the  
   probabibility to be observed in state j at the second wave    Revision 1.135  2009/10/29 15:33:14  brouard
   conditional to be observed in state i at the first wave. Therefore    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.134  2009/10/29 13:18:53  brouard
   complex model than "constant and age", you should modify the program    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Revision 1.133  2009/07/06 10:21:25  brouard
   convergence.    just nforces
   
   The advantage of this computer programme, compared to a simple    Revision 1.132  2009/07/06 08:22:05  brouard
   multinomial logistic model, is clear when the delay between waves is not    Many tings
   identical for each individual. Also, if a individual missed an  
   intermediate interview, the information is lost, but taken into    Revision 1.131  2009/06/20 16:22:47  brouard
   account using an interpolation or extrapolation.      Some dimensions resccaled
   
   hPijx is the probability to be observed in state i at age x+h    Revision 1.130  2009/05/26 06:44:34  brouard
   conditional to the observed state i at age x. The delay 'h' can be    (Module): Max Covariate is now set to 20 instead of 8. A
   split into an exact number (nh*stepm) of unobserved intermediate    lot of cleaning with variables initialized to 0. Trying to make
   states. This elementary transition (by month or quarter trimester,    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.129  2007/08/31 13:49:27  lievre
   and the contribution of each individual to the likelihood is simply    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
   hPijx.  
     Revision 1.128  2006/06/30 13:02:05  brouard
   Also this programme outputs the covariance matrix of the parameters but also    (Module): Clarifications on computing e.j
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.127  2006/04/28 18:11:50  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    (Module): Yes the sum of survivors was wrong since
            Institut national d'études démographiques, Paris.    imach-114 because nhstepm was no more computed in the age
   This software have been partly granted by Euro-REVES, a concerted action    loop. Now we define nhstepma in the age loop.
   from the European Union.    (Module): In order to speed up (in case of numerous covariates) we
   It is copyrighted identically to a GNU software product, ie programme and    compute health expectancies (without variances) in a first step
   software can be distributed freely for non commercial use. Latest version    and then all the health expectancies with variances or standard
   can be accessed at http://euroreves.ined.fr/imach .    deviation (needs data from the Hessian matrices) which slows the
   **********************************************************************/    computation.
      In the future we should be able to stop the program is only health
 #include <math.h>    expectancies and graph are needed without standard deviations.
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.126  2006/04/28 17:23:28  brouard
 #include <unistd.h>    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
 #define MAXLINE 256    loop. Now we define nhstepma in the age loop.
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    Version 0.98h
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.125  2006/04/04 15:20:31  lievre
 #define windows    Errors in calculation of health expectancies. Age was not initialized.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Forecasting file added.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.124  2006/03/22 17:13:53  lievre
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Parameters are printed with %lf instead of %f (more numbers after the comma).
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    The log-likelihood is printed in the log file
   
 #define NINTERVMAX 8    Revision 1.123  2006/03/20 10:52:43  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    * imach.c (Module): <title> changed, corresponds to .htm file
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    name. <head> headers where missing.
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    * imach.c (Module): Weights can have a decimal point as for
 #define YEARM 12. /* Number of months per year */    English (a comma might work with a correct LC_NUMERIC environment,
 #define AGESUP 130    otherwise the weight is truncated).
 #define AGEBASE 40    Modification of warning when the covariates values are not 0 or
     1.
     Version 0.98g
 int erreur; /* Error number */  
 int nvar;    Revision 1.122  2006/03/20 09:45:41  brouard
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    (Module): Weights can have a decimal point as for
 int npar=NPARMAX;    English (a comma might work with a correct LC_NUMERIC environment,
 int nlstate=2; /* Number of live states */    otherwise the weight is truncated).
 int ndeath=1; /* Number of dead states */    Modification of warning when the covariates values are not 0 or
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    1.
 int popbased=0;    Version 0.98g
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.121  2006/03/16 17:45:01  lievre
 int maxwav; /* Maxim number of waves */    * imach.c (Module): Comments concerning covariates added
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    * imach.c (Module): refinements in the computation of lli if
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    status=-2 in order to have more reliable computation if stepm is
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    not 1 month. Version 0.98f
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.120  2006/03/16 15:10:38  lievre
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    (Module): refinements in the computation of lli if
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    status=-2 in order to have more reliable computation if stepm is
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    not 1 month. Version 0.98f
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.119  2006/03/15 17:42:26  brouard
  FILE  *ficresvij;    (Module): Bug if status = -2, the loglikelihood was
   char fileresv[FILENAMELENGTH];    computed as likelihood omitting the logarithm. Version O.98e
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Revision 1.118  2006/03/14 18:20:07  brouard
     (Module): varevsij Comments added explaining the second
 #define NR_END 1    table of variances if popbased=1 .
 #define FREE_ARG char*    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #define FTOL 1.0e-10    (Module): Function pstamp added
     (Module): Version 0.98d
 #define NRANSI  
 #define ITMAX 200    Revision 1.117  2006/03/14 17:16:22  brouard
     (Module): varevsij Comments added explaining the second
 #define TOL 2.0e-4    table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #define CGOLD 0.3819660    (Module): Function pstamp added
 #define ZEPS 1.0e-10    (Module): Version 0.98d
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.116  2006/03/06 10:29:27  brouard
 #define GOLD 1.618034    (Module): Variance-covariance wrong links and
 #define GLIMIT 100.0    varian-covariance of ej. is needed (Saito).
 #define TINY 1.0e-20  
     Revision 1.115  2006/02/27 12:17:45  brouard
 static double maxarg1,maxarg2;    (Module): One freematrix added in mlikeli! 0.98c
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.114  2006/02/26 12:57:58  brouard
      (Module): Some improvements in processing parameter
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    filename with strsep.
 #define rint(a) floor(a+0.5)  
     Revision 1.113  2006/02/24 14:20:24  brouard
 static double sqrarg;    (Module): Memory leaks checks with valgrind and:
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    datafile was not closed, some imatrix were not freed and on matrix
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    allocation too.
   
 int imx;    Revision 1.112  2006/01/30 09:55:26  brouard
 int stepm;    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.111  2006/01/25 20:38:18  brouard
 int m,nb;    (Module): Lots of cleaning and bugs added (Gompertz)
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    (Module): Comments can be added in data file. Missing date values
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    can be a simple dot '.'.
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;    Revision 1.110  2006/01/25 00:51:50  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 double *weight;  
 int **s; /* Status */    Revision 1.109  2006/01/24 19:37:15  brouard
 double *agedc, **covar, idx;    (Module): Comments (lines starting with a #) are allowed in data.
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.108  2006/01/19 18:05:42  lievre
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Gnuplot problem appeared...
 double ftolhess; /* Tolerance for computing hessian */    To be fixed
   
 /**************** split *************************/    Revision 1.107  2006/01/19 16:20:37  brouard
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Test existence of gnuplot in imach path
 {  
    char *s;                             /* pointer */    Revision 1.106  2006/01/19 13:24:36  brouard
    int  l1, l2;                         /* length counters */    Some cleaning and links added in html output
   
    l1 = strlen( path );                 /* length of path */    Revision 1.105  2006/01/05 20:23:19  lievre
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    *** empty log message ***
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */    Revision 1.104  2005/09/30 16:11:43  lievre
 #else    (Module): sump fixed, loop imx fixed, and simplifications.
    s = strrchr( path, '/' );            /* find last / */    (Module): If the status is missing at the last wave but we know
 #endif    that the person is alive, then we can code his/her status as -2
    if ( s == NULL ) {                   /* no directory, so use current */    (instead of missing=-1 in earlier versions) and his/her
 #if     defined(__bsd__)                /* get current working directory */    contributions to the likelihood is 1 - Prob of dying from last
       extern char       *getwd( );    health status (= 1-p13= p11+p12 in the easiest case of somebody in
     the healthy state at last known wave). Version is 0.98
       if ( getwd( dirc ) == NULL ) {  
 #else    Revision 1.103  2005/09/30 15:54:49  lievre
       extern char       *getcwd( );    (Module): sump fixed, loop imx fixed, and simplifications.
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.102  2004/09/15 17:31:30  brouard
 #endif    Add the possibility to read data file including tab characters.
          return( GLOCK_ERROR_GETCWD );  
       }    Revision 1.101  2004/09/15 10:38:38  brouard
       strcpy( name, path );             /* we've got it */    Fix on curr_time
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Revision 1.100  2004/07/12 18:29:06  brouard
       l2 = strlen( s );                 /* length of filename */    Add version for Mac OS X. Just define UNIX in Makefile
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Revision 1.99  2004/06/05 08:57:40  brouard
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    *** empty log message ***
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.98  2004/05/16 15:05:56  brouard
    l1 = strlen( dirc );                 /* length of directory */    New version 0.97 . First attempt to estimate force of mortality
 #ifdef windows    directly from the data i.e. without the need of knowing the health
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    state at each age, but using a Gompertz model: log u =a + b*age .
 #else    This is the basic analysis of mortality and should be done before any
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    other analysis, in order to test if the mortality estimated from the
 #endif    cross-longitudinal survey is different from the mortality estimated
    s = strrchr( name, '.' );            /* find last / */    from other sources like vital statistic data.
    s++;  
    strcpy(ext,s);                       /* save extension */    The same imach parameter file can be used but the option for mle should be -3.
    l1= strlen( name);  
    l2= strlen( s)+1;    Agnès, who wrote this part of the code, tried to keep most of the
    strncpy( finame, name, l1-l2);    former routines in order to include the new code within the former code.
    finame[l1-l2]= 0;  
    return( 0 );                         /* we're done */    The output is very simple: only an estimate of the intercept and of
 }    the slope with 95% confident intervals.
   
     Current limitations:
 /******************************************/    A) Even if you enter covariates, i.e. with the
     model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 void replace(char *s, char*t)    B) There is no computation of Life Expectancy nor Life Table.
 {  
   int i;    Revision 1.97  2004/02/20 13:25:42  lievre
   int lg=20;    Version 0.96d. Population forecasting command line is (temporarily)
   i=0;    suppressed.
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.96  2003/07/15 15:38:55  brouard
     (s[i] = t[i]);    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     if (t[i]== '\\') s[i]='/';    rewritten within the same printf. Workaround: many printfs.
   }  
 }    Revision 1.95  2003/07/08 07:54:34  brouard
     * imach.c (Repository):
 int nbocc(char *s, char occ)    (Repository): Using imachwizard code to output a more meaningful covariance
 {    matrix (cov(a12,c31) instead of numbers.
   int i,j=0;  
   int lg=20;    Revision 1.94  2003/06/27 13:00:02  brouard
   i=0;    Just cleaning
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {    Revision 1.93  2003/06/25 16:33:55  brouard
   if  (s[i] == occ ) j++;    (Module): On windows (cygwin) function asctime_r doesn't
   }    exist so I changed back to asctime which exists.
   return j;    (Module): Version 0.96b
 }  
     Revision 1.92  2003/06/25 16:30:45  brouard
 void cutv(char *u,char *v, char*t, char occ)    (Module): On windows (cygwin) function asctime_r doesn't
 {    exist so I changed back to asctime which exists.
   int i,lg,j,p=0;  
   i=0;    Revision 1.91  2003/06/25 15:30:29  brouard
   for(j=0; j<=strlen(t)-1; j++) {    * imach.c (Repository): Duplicated warning errors corrected.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    (Repository): Elapsed time after each iteration is now output. It
   }    helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
   lg=strlen(t);    concerning matrix of covariance. It has extension -cov.htm.
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);    Revision 1.90  2003/06/24 12:34:15  brouard
   }    (Module): Some bugs corrected for windows. Also, when
      u[p]='\0';    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    Revision 1.89  2003/06/24 12:30:52  brouard
   }    (Module): Some bugs corrected for windows. Also, when
 }    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 /********************** nrerror ********************/  
     Revision 1.88  2003/06/23 17:54:56  brouard
 void nrerror(char error_text[])    * 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.
 {  
   fprintf(stderr,"ERREUR ...\n");    Revision 1.87  2003/06/18 12:26:01  brouard
   fprintf(stderr,"%s\n",error_text);    Version 0.96
   exit(1);  
 }    Revision 1.86  2003/06/17 20:04:08  brouard
 /*********************** vector *******************/    (Module): Change position of html and gnuplot routines and added
 double *vector(int nl, int nh)    routine fileappend.
 {  
   double *v;    Revision 1.85  2003/06/17 13:12:43  brouard
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    * imach.c (Repository): Check when date of death was earlier that
   if (!v) nrerror("allocation failure in vector");    current date of interview. It may happen when the death was just
   return v-nl+NR_END;    prior to the death. In this case, dh was negative and likelihood
 }    was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
 /************************ free vector ******************/    interview.
 void free_vector(double*v, int nl, int nh)    (Repository): Because some people have very long ID (first column)
 {    we changed int to long in num[] and we added a new lvector for
   free((FREE_ARG)(v+nl-NR_END));    memory allocation. But we also truncated to 8 characters (left
 }    truncation)
     (Repository): No more line truncation errors.
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)    Revision 1.84  2003/06/13 21:44:43  brouard
 {    * imach.c (Repository): Replace "freqsummary" at a correct
   int *v;    place. It differs from routine "prevalence" which may be called
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    many times. Probs is memory consuming and must be used with
   if (!v) nrerror("allocation failure in ivector");    parcimony.
   return v-nl+NR_END;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 }  
     Revision 1.83  2003/06/10 13:39:11  lievre
 /******************free ivector **************************/    *** empty log message ***
 void free_ivector(int *v, long nl, long nh)  
 {    Revision 1.82  2003/06/05 15:57:20  brouard
   free((FREE_ARG)(v+nl-NR_END));    Add log in  imach.c and  fullversion number is now printed.
 }  
   */
 /******************* imatrix *******************************/  /*
 int **imatrix(long nrl, long nrh, long ncl, long nch)     Interpolated Markov Chain
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {    Short summary of the programme:
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    
   int **m;    This program computes Healthy Life Expectancies from
      cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   /* allocate pointers to rows */    first survey ("cross") where individuals from different ages are
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    interviewed on their health status or degree of disability (in the
   if (!m) nrerror("allocation failure 1 in matrix()");    case of a health survey which is our main interest) -2- at least a
   m += NR_END;    second wave of interviews ("longitudinal") which measure each change
   m -= nrl;    (if any) in individual health status.  Health expectancies are
      computed from the time spent in each health state according to a
      model. More health states you consider, more time is necessary to reach the
   /* allocate rows and set pointers to them */    Maximum Likelihood of the parameters involved in the model.  The
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    simplest model is the multinomial logistic model where pij is the
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    probability to be observed in state j at the second wave
   m[nrl] += NR_END;    conditional to be observed in state i at the first wave. Therefore
   m[nrl] -= ncl;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
      'age' is age and 'sex' is a covariate. If you want to have a more
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    complex model than "constant and age", you should modify the program
      where the markup *Covariates have to be included here again* invites
   /* return pointer to array of pointers to rows */    you to do it.  More covariates you add, slower the
   return m;    convergence.
 }  
     The advantage of this computer programme, compared to a simple
 /****************** free_imatrix *************************/    multinomial logistic model, is clear when the delay between waves is not
 void free_imatrix(m,nrl,nrh,ncl,nch)    identical for each individual. Also, if a individual missed an
       int **m;    intermediate interview, the information is lost, but taken into
       long nch,ncl,nrh,nrl;    account using an interpolation or extrapolation.  
      /* free an int matrix allocated by imatrix() */  
 {    hPijx is the probability to be observed in state i at age x+h
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    conditional to the observed state i at age x. The delay 'h' can be
   free((FREE_ARG) (m+nrl-NR_END));    split into an exact number (nh*stepm) of unobserved intermediate
 }    states. This elementary transition (by month, quarter,
     semester or year) is modelled as a multinomial logistic.  The hPx
 /******************* matrix *******************************/    matrix is simply the matrix product of nh*stepm elementary matrices
 double **matrix(long nrl, long nrh, long ncl, long nch)    and the contribution of each individual to the likelihood is simply
 {    hPijx.
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the period (stable) prevalence. 
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    
   if (!m) nrerror("allocation failure 1 in matrix()");    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   m += NR_END;             Institut national d'études démographiques, Paris.
   m -= nrl;    This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    It is copyrighted identically to a GNU software product, ie programme and
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    software can be distributed freely for non commercial use. Latest version
   m[nrl] += NR_END;    can be accessed at http://euroreves.ined.fr/imach .
   m[nrl] -= ncl;  
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   return m;    
 }    **********************************************************************/
   /*
 /*************************free matrix ************************/    main
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    read parameterfile
 {    read datafile
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    concatwav
   free((FREE_ARG)(m+nrl-NR_END));    freqsummary
 }    if (mle >= 1)
       mlikeli
 /******************* ma3x *******************************/    print results files
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    if mle==1 
 {       computes hessian
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    read end of parameter file: agemin, agemax, bage, fage, estepm
   double ***m;        begin-prev-date,...
     open gnuplot file
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    open html file
   if (!m) nrerror("allocation failure 1 in matrix()");    period (stable) prevalence
   m += NR_END;     for age prevalim()
   m -= nrl;    h Pij x
     variance of p varprob
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    forecasting if prevfcast==1 prevforecast call prevalence()
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    health expectancies
   m[nrl] += NR_END;    Variance-covariance of DFLE
   m[nrl] -= ncl;    prevalence()
      movingaverage()
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    varevsij() 
     if popbased==1 varevsij(,popbased)
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    total life expectancies
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    Variance of period (stable) prevalence
   m[nrl][ncl] += NR_END;   end
   m[nrl][ncl] -= nll;  */
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;  
    
   for (i=nrl+1; i<=nrh; i++) {   
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #include <math.h>
     for (j=ncl+1; j<=nch; j++)  #include <stdio.h>
       m[i][j]=m[i][j-1]+nlay;  #include <stdlib.h>
   }  #include <string.h>
   return m;  #include <unistd.h>
 }  
   #include <limits.h>
 /*************************free ma3x ************************/  #include <sys/types.h>
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  #include <sys/stat.h>
 {  #include <errno.h>
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  extern int errno;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  /* #include <sys/time.h> */
 }  #include <time.h>
   #include "timeval.h"
 /***************** f1dim *************************/  
 extern int ncom;  #ifdef GSL
 extern double *pcom,*xicom;  #include <gsl/gsl_errno.h>
 extern double (*nrfunc)(double []);  #include <gsl/gsl_multimin.h>
    #endif
 double f1dim(double x)  
 {  /* #include <libintl.h> */
   int j;  /* #define _(String) gettext (String) */
   double f;  
   double *xt;  #define MAXLINE 256
    
   xt=vector(1,ncom);  #define GNUPLOTPROGRAM "gnuplot"
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   f=(*nrfunc)(xt);  #define FILENAMELENGTH 132
   free_vector(xt,1,ncom);  
   return f;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 }  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 /*****************brent *************************/  #define MAXPARM 128 /* Maximum number of parameters for the optimization */
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 {  
   int iter;  #define NINTERVMAX 8
   double a,b,d,etemp;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   double fu,fv,fw,fx;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   double ftemp;  #define NCOVMAX 20 /* Maximum number of covariates */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  #define MAXN 20000
   double e=0.0;  #define YEARM 12. /* Number of months per year */
    #define AGESUP 130
   a=(ax < cx ? ax : cx);  #define AGEBASE 40
   b=(ax > cx ? ax : cx);  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   x=w=v=bx;  #ifdef UNIX
   fw=fv=fx=(*f)(x);  #define DIRSEPARATOR '/'
   for (iter=1;iter<=ITMAX;iter++) {  #define CHARSEPARATOR "/"
     xm=0.5*(a+b);  #define ODIRSEPARATOR '\\'
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  #else
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  #define DIRSEPARATOR '\\'
     printf(".");fflush(stdout);  #define CHARSEPARATOR "\\"
 #ifdef DEBUG  #define ODIRSEPARATOR '/'
     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);  #endif
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif  /* $Id$ */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  /* $State$ */
       *xmin=x;  
       return fx;  char version[]="Imach version 0.98m, April 2010, INED-EUROREVES-Institut de longevite ";
     }  char fullversion[]="$Revision$ $Date$"; 
     ftemp=fu;  char strstart[80];
     if (fabs(e) > tol1) {  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
       r=(x-w)*(fx-fv);  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
       q=(x-v)*(fx-fw);  int nvar=0, nforce=0; /* Number of variables, number of forces */
       p=(x-v)*q-(x-w)*r;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
       q=2.0*(q-r);  int npar=NPARMAX;
       if (q > 0.0) p = -p;  int nlstate=2; /* Number of live states */
       q=fabs(q);  int ndeath=1; /* Number of dead states */
       etemp=e;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       e=d;  int popbased=0;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  int *wav; /* Number of waves for this individuual 0 is possible */
       else {  int maxwav=0; /* Maxim number of waves */
         d=p/q;  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
         u=x+d;  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
         if (u-a < tol2 || b-u < tol2)  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
           d=SIGN(tol1,xm-x);                     to the likelihood and the sum of weights (done by funcone)*/
       }  int mle=1, weightopt=0;
     } else {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     }  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     fu=(*f)(u);  double jmean=1; /* Mean space between 2 waves */
     if (fu <= fx) {  double **oldm, **newm, **savm; /* Working pointers to matrices */
       if (u >= x) a=x; else b=x;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       SHFT(v,w,x,u)  /*FILE *fic ; */ /* Used in readdata only */
         SHFT(fv,fw,fx,fu)  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
         } else {  FILE *ficlog, *ficrespow;
           if (u < x) a=u; else b=u;  int globpr=0; /* Global variable for printing or not */
           if (fu <= fw || w == x) {  double fretone; /* Only one call to likelihood */
             v=w;  long ipmx=0; /* Number of contributions */
             w=u;  double sw; /* Sum of weights */
             fv=fw;  char filerespow[FILENAMELENGTH];
             fw=fu;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
           } else if (fu <= fv || v == x || v == w) {  FILE *ficresilk;
             v=u;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
             fv=fu;  FILE *ficresprobmorprev;
           }  FILE *fichtm, *fichtmcov; /* Html File */
         }  FILE *ficreseij;
   }  char filerese[FILENAMELENGTH];
   nrerror("Too many iterations in brent");  FILE *ficresstdeij;
   *xmin=x;  char fileresstde[FILENAMELENGTH];
   return fx;  FILE *ficrescveij;
 }  char filerescve[FILENAMELENGTH];
   FILE  *ficresvij;
 /****************** mnbrak ***********************/  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  char fileresvpl[FILENAMELENGTH];
             double (*func)(double))  char title[MAXLINE];
 {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   double ulim,u,r,q, dum;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   double fu;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
    char command[FILENAMELENGTH];
   *fa=(*func)(*ax);  int  outcmd=0;
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  char filelog[FILENAMELENGTH]; /* Log file */
       }  char filerest[FILENAMELENGTH];
   *cx=(*bx)+GOLD*(*bx-*ax);  char fileregp[FILENAMELENGTH];
   *fc=(*func)(*cx);  char popfile[FILENAMELENGTH];
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  struct timezone tzp;
     ulim=(*bx)+GLIMIT*(*cx-*bx);  extern int gettimeofday();
     if ((*bx-u)*(u-*cx) > 0.0) {  struct tm tmg, tm, tmf, *gmtime(), *localtime();
       fu=(*func)(u);  long time_value;
     } else if ((*cx-u)*(u-ulim) > 0.0) {  extern long time();
       fu=(*func)(u);  char strcurr[80], strfor[80];
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  char *endptr;
           SHFT(*fb,*fc,fu,(*func)(u))  long lval;
           }  double dval;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  #define NR_END 1
       fu=(*func)(u);  #define FREE_ARG char*
     } else {  #define FTOL 1.0e-10
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);  #define NRANSI 
     }  #define ITMAX 200 
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)  #define TOL 2.0e-4 
       }  
 }  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 /*************** linmin ************************/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
 int ncom;  #define GOLD 1.618034 
 double *pcom,*xicom;  #define GLIMIT 100.0 
 double (*nrfunc)(double []);  #define TINY 1.0e-20 
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  static double maxarg1,maxarg2;
 {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   double brent(double ax, double bx, double cx,  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
                double (*f)(double), double tol, double *xmin);    
   double f1dim(double x);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  #define rint(a) floor(a+0.5)
               double *fc, double (*func)(double));  
   int j;  static double sqrarg;
   double xx,xmin,bx,ax;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   double fx,fb,fa;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
    int agegomp= AGEGOMP;
   ncom=n;  
   pcom=vector(1,n);  int imx; 
   xicom=vector(1,n);  int stepm=1;
   nrfunc=func;  /* Stepm, step in month: minimum step interpolation*/
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];  int estepm;
     xicom[j]=xi[j];  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   }  
   ax=0.0;  int m,nb;
   xx=1.0;  long *num;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 #ifdef DEBUG  double **pmmij, ***probs;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  double *ageexmed,*agecens;
 #endif  double dateintmean=0;
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;  double *weight;
     p[j] += xi[j];  int **s; /* Status */
   }  double *agedc, **covar, idx;
   free_vector(xicom,1,n);  int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   free_vector(pcom,1,n);  double *lsurv, *lpop, *tpop;
 }  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 /*************** powell ************************/  double ftolhess; /* Tolerance for computing hessian */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  
             double (*func)(double []))  /**************** split *************************/
 {  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   void linmin(double p[], double xi[], int n, double *fret,  {
               double (*func)(double []));    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
   int i,ibig,j;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   double del,t,*pt,*ptt,*xit;    */ 
   double fp,fptt;    char  *ss;                            /* pointer */
   double *xits;    int   l1, l2;                         /* length counters */
   pt=vector(1,n);  
   ptt=vector(1,n);    l1 = strlen(path );                   /* length of path */
   xit=vector(1,n);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   xits=vector(1,n);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   *fret=(*func)(p);    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   for (j=1;j<=n;j++) pt[j]=p[j];      strcpy( name, path );               /* we got the fullname name because no directory */
   for (*iter=1;;++(*iter)) {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
     fp=(*fret);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     ibig=0;      /* get current working directory */
     del=0.0;      /*    extern  char* getcwd ( char *buf , int len);*/
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     for (i=1;i<=n;i++)        return( GLOCK_ERROR_GETCWD );
       printf(" %d %.12f",i, p[i]);      }
     printf("\n");      /* got dirc from getcwd*/
     for (i=1;i<=n;i++) {      printf(" DIRC = %s \n",dirc);
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    } else {                              /* strip direcotry from path */
       fptt=(*fret);      ss++;                               /* after this, the filename */
 #ifdef DEBUG      l2 = strlen( ss );                  /* length of filename */
       printf("fret=%lf \n",*fret);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 #endif      strcpy( name, ss );         /* save file name */
       printf("%d",i);fflush(stdout);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       linmin(p,xit,n,fret,func);      dirc[l1-l2] = 0;                    /* add zero */
       if (fabs(fptt-(*fret)) > del) {      printf(" DIRC2 = %s \n",dirc);
         del=fabs(fptt-(*fret));    }
         ibig=i;    /* We add a separator at the end of dirc if not exists */
       }    l1 = strlen( dirc );                  /* length of directory */
 #ifdef DEBUG    if( dirc[l1-1] != DIRSEPARATOR ){
       printf("%d %.12e",i,(*fret));      dirc[l1] =  DIRSEPARATOR;
       for (j=1;j<=n;j++) {      dirc[l1+1] = 0; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      printf(" DIRC3 = %s \n",dirc);
         printf(" x(%d)=%.12e",j,xit[j]);    }
       }    ss = strrchr( name, '.' );            /* find last / */
       for(j=1;j<=n;j++)    if (ss >0){
         printf(" p=%.12e",p[j]);      ss++;
       printf("\n");      strcpy(ext,ss);                     /* save extension */
 #endif      l1= strlen( name);
     }      l2= strlen(ss)+1;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      strncpy( finame, name, l1-l2);
 #ifdef DEBUG      finame[l1-l2]= 0;
       int k[2],l;    }
       k[0]=1;  
       k[1]=-1;    return( 0 );                          /* we're done */
       printf("Max: %.12e",(*func)(p));  }
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  
       printf("\n");  /******************************************/
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {  void replace_back_to_slash(char *s, char*t)
           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]);    int i;
         }    int lg=0;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    i=0;
       }    lg=strlen(t);
 #endif    for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
       free_vector(xit,1,n);    }
       free_vector(xits,1,n);  }
       free_vector(ptt,1,n);  
       free_vector(pt,1,n);  char *trimbb(char *out, char *in)
       return;  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
     }    char *s;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    s=out;
     for (j=1;j<=n;j++) {    while (*in != '\0'){
       ptt[j]=2.0*p[j]-pt[j];      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
       xit[j]=p[j]-pt[j];        in++;
       pt[j]=p[j];      }
     }      *out++ = *in++;
     fptt=(*func)(ptt);    }
     if (fptt < fp) {    *out='\0';
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    return s;
       if (t < 0.0) {  }
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {  char *cutv(char *blocc, char *alocc, char *in, char occ)
           xi[j][ibig]=xi[j][n];  {
           xi[j][n]=xit[j];    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
         }       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
 #ifdef DEBUG       gives blocc="abcdef2ghi" and alocc="j".
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);       If occ is not found blocc is null and alocc is equal to in. Returns alocc
         for(j=1;j<=n;j++)    */
           printf(" %.12e",xit[j]);    char *s, *t;
         printf("\n");    t=in;s=in;
 #endif    while (*in != '\0'){
       }      while( *in == occ){
     }        *blocc++ = *in++;
   }        s=in;
 }      }
       *blocc++ = *in++;
 /**** Prevalence limit ****************/    }
     if (s == t) /* occ not found */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      *(blocc-(in-s))='\0';
 {    else
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      *(blocc-(in-s)-1)='\0';
      matrix by transitions matrix until convergence is reached */    in=s;
     while ( *in != '\0'){
   int i, ii,j,k;      *alocc++ = *in++;
   double min, max, maxmin, maxmax,sumnew=0.;    }
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();    *alocc='\0';
   double **newm;    return s;
   double agefin, delaymax=50 ; /* Max number of years to converge */  }
   
   for (ii=1;ii<=nlstate+ndeath;ii++)  int nbocc(char *s, char occ)
     for (j=1;j<=nlstate+ndeath;j++){  {
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    int i,j=0;
     }    int lg=20;
     i=0;
    cov[1]=1.;    lg=strlen(s);
      for(i=0; i<= lg; i++) {
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    if  (s[i] == occ ) j++;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    }
     newm=savm;    return j;
     /* Covariates have to be included here again */  }
      cov[2]=agefin;  
    /* void cutv(char *u,char *v, char*t, char occ) */
       for (k=1; k<=cptcovn;k++) {  /* { */
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
       }  /*      gives u="abcdef2ghi" and v="j" *\/ */
       for (k=1; k<=cptcovage;k++)  /*   int i,lg,j,p=0; */
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /*   i=0; */
       for (k=1; k<=cptcovprod;k++)  /*   lg=strlen(t); */
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  /*   for(j=0; j<=lg-1; j++) { */
   /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  /*   } */
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  
   /*   for(j=0; j<p; j++) { */
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  /*     (u[j] = t[j]); */
   /*   } */
     savm=oldm;  /*      u[p]='\0'; */
     oldm=newm;  
     maxmax=0.;  /*    for(j=0; j<= lg; j++) { */
     for(j=1;j<=nlstate;j++){  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
       min=1.;  /*   } */
       max=0.;  /* } */
       for(i=1; i<=nlstate; i++) {  
         sumnew=0;  /********************** nrerror ********************/
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  void nrerror(char error_text[])
         max=FMAX(max,prlim[i][j]);  {
         min=FMIN(min,prlim[i][j]);    fprintf(stderr,"ERREUR ...\n");
       }    fprintf(stderr,"%s\n",error_text);
       maxmin=max-min;    exit(EXIT_FAILURE);
       maxmax=FMAX(maxmax,maxmin);  }
     }  /*********************** vector *******************/
     if(maxmax < ftolpl){  double *vector(int nl, int nh)
       return prlim;  {
     }    double *v;
   }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 }    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
 /*************** transition probabilities ***************/  }
   
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  /************************ free vector ******************/
 {  void free_vector(double*v, int nl, int nh)
   double s1, s2;  {
   /*double t34;*/    free((FREE_ARG)(v+nl-NR_END));
   int i,j,j1, nc, ii, jj;  }
   
     for(i=1; i<= nlstate; i++){  /************************ivector *******************************/
     for(j=1; j<i;j++){  int *ivector(long nl,long nh)
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  {
         /*s2 += param[i][j][nc]*cov[nc];*/    int *v;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    if (!v) nrerror("allocation failure in ivector");
       }    return v-nl+NR_END;
       ps[i][j]=s2;  }
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  
     }  /******************free ivector **************************/
     for(j=i+1; j<=nlstate+ndeath;j++){  void free_ivector(int *v, long nl, long nh)
       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];    free((FREE_ARG)(v+nl-NR_END));
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  }
       }  
       ps[i][j]=s2;  /************************lvector *******************************/
     }  long *lvector(long nl,long nh)
   }  {
     /*ps[3][2]=1;*/    long *v;
     v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   for(i=1; i<= nlstate; i++){    if (!v) nrerror("allocation failure in ivector");
      s1=0;    return v-nl+NR_END;
     for(j=1; j<i; j++)  }
       s1+=exp(ps[i][j]);  
     for(j=i+1; j<=nlstate+ndeath; j++)  /******************free lvector **************************/
       s1+=exp(ps[i][j]);  void free_lvector(long *v, long nl, long nh)
     ps[i][i]=1./(s1+1.);  {
     for(j=1; j<i; j++)    free((FREE_ARG)(v+nl-NR_END));
       ps[i][j]= exp(ps[i][j])*ps[i][i];  }
     for(j=i+1; j<=nlstate+ndeath; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /******************* imatrix *******************************/
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   } /* end i */       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   { 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     for(jj=1; jj<= nlstate+ndeath; jj++){    int **m; 
       ps[ii][jj]=0;    
       ps[ii][ii]=1;    /* allocate pointers to rows */ 
     }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   }    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
     m -= nrl; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    
     for(jj=1; jj<= nlstate+ndeath; jj++){    
      printf("%lf ",ps[ii][jj]);    /* allocate rows and set pointers to them */ 
    }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     printf("\n ");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     }    m[nrl] += NR_END; 
     printf("\n ");printf("%lf ",cov[2]);*/    m[nrl] -= ncl; 
 /*    
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   goto end;*/    
     return ps;    /* return pointer to array of pointers to rows */ 
 }    return m; 
   } 
 /**************** Product of 2 matrices ******************/  
   /****************** free_imatrix *************************/
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  void free_imatrix(m,nrl,nrh,ncl,nch)
 {        int **m;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        long nch,ncl,nrh,nrl; 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */       /* free an int matrix allocated by imatrix() */ 
   /* in, b, out are matrice of pointers which should have been initialized  { 
      before: only the contents of out is modified. The function returns    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
      a pointer to pointers identical to out */    free((FREE_ARG) (m+nrl-NR_END)); 
   long i, j, k;  } 
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++)  /******************* matrix *******************************/
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  double **matrix(long nrl, long nrh, long ncl, long nch)
         out[i][k] +=in[i][j]*b[j][k];  {
     long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   return out;    double **m;
 }  
     m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 /************* Higher Matrix Product ***************/    m += NR_END;
     m -= nrl;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      duration (i.e. until    m[nrl] += NR_END;
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    m[nrl] -= ncl;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  
      (typically every 2 years instead of every month which is too big).    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
      Model is determined by parameters x and covariates have to be    return m;
      included manually here.    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
      */
      */  }
   
   int i, j, d, h, k;  /*************************free matrix ************************/
   double **out, cov[NCOVMAX];  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double **newm;  {
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
   /* Hstepm could be zero and should return the unit matrix */    free((FREE_ARG)(m+nrl-NR_END));
   for (i=1;i<=nlstate+ndeath;i++)  }
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);  /******************* ma3x *******************************/
       po[i][j][0]=(i==j ? 1.0 : 0.0);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     }  {
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   for(h=1; h <=nhstepm; h++){    double ***m;
     for(d=1; d <=hstepm; d++){  
       newm=savm;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       /* Covariates have to be included here again */    if (!m) nrerror("allocation failure 1 in matrix()");
       cov[1]=1.;    m += NR_END;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    m -= nrl;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
       for (k=1; k<=cptcovage;k++)    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         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;
   
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    m[nrl][ncl] += NR_END;
       savm=oldm;    m[nrl][ncl] -= nll;
       oldm=newm;    for (j=ncl+1; j<=nch; j++) 
     }      m[nrl][j]=m[nrl][j-1]+nlay;
     for(i=1; i<=nlstate+ndeath; i++)    
       for(j=1;j<=nlstate+ndeath;j++) {    for (i=nrl+1; i<=nrh; i++) {
         po[i][j][h]=newm[i][j];      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      for (j=ncl+1; j<=nch; j++) 
          */        m[i][j]=m[i][j-1]+nlay;
       }    }
   } /* end h */    return m; 
   return po;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 }             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     */
   }
 /*************** log-likelihood *************/  
 double func( double *x)  /*************************free ma3x ************************/
 {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   int i, ii, j, k, mi, d, kk;  {
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   double **out;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double sw; /* Sum of weights */    free((FREE_ARG)(m+nrl-NR_END));
   double lli; /* Individual log likelihood */  }
   long ipmx;  
   /*extern weight */  /*************** function subdirf ***********/
   /* We are differentiating ll according to initial status */  char *subdirf(char fileres[])
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  {
   /*for(i=1;i<imx;i++)    /* Caution optionfilefiname is hidden */
     printf(" %d\n",s[4][i]);    strcpy(tmpout,optionfilefiname);
   */    strcat(tmpout,"/"); /* Add to the right */
   cov[1]=1.;    strcat(tmpout,fileres);
     return tmpout;
   for(k=1; k<=nlstate; k++) ll[k]=0.;  }
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  /*************** function subdirf2 ***********/
     for(mi=1; mi<= wav[i]-1; mi++){  char *subdirf2(char fileres[], char *preop)
       for (ii=1;ii<=nlstate+ndeath;ii++)  {
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    
       for(d=0; d<dh[mi][i]; d++){    /* Caution optionfilefiname is hidden */
         newm=savm;    strcpy(tmpout,optionfilefiname);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    strcat(tmpout,"/");
         for (kk=1; kk<=cptcovage;kk++) {    strcat(tmpout,preop);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    strcat(tmpout,fileres);
         }    return tmpout;
          }
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  /*************** function subdirf3 ***********/
         savm=oldm;  char *subdirf3(char fileres[], char *preop, char *preop2)
         oldm=newm;  {
            
            /* Caution optionfilefiname is hidden */
       } /* end mult */    strcpy(tmpout,optionfilefiname);
          strcat(tmpout,"/");
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    strcat(tmpout,preop);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    strcat(tmpout,preop2);
       ipmx +=1;    strcat(tmpout,fileres);
       sw += weight[i];    return tmpout;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  }
     } /* end of wave */  
   } /* end of individual */  /***************** f1dim *************************/
   extern int ncom; 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  extern double *pcom,*xicom;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  extern double (*nrfunc)(double []); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */   
   return -l;  double f1dim(double x) 
 }  { 
     int j; 
     double f;
 /*********** Maximum Likelihood Estimation ***************/    double *xt; 
    
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    xt=vector(1,ncom); 
 {    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   int i,j, iter;    f=(*nrfunc)(xt); 
   double **xi,*delti;    free_vector(xt,1,ncom); 
   double fret;    return f; 
   xi=matrix(1,npar,1,npar);  } 
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)  /*****************brent *************************/
       xi[i][j]=(i==j ? 1.0 : 0.0);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   printf("Powell\n");  { 
   powell(p,xi,npar,ftol,&iter,&fret,func);    int iter; 
     double a,b,d,etemp;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    double fu,fv,fw,fx;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    double ftemp;
     double p,q,r,tol1,tol2,u,v,w,x,xm; 
 }    double e=0.0; 
    
 /**** Computes Hessian and covariance matrix ***/    a=(ax < cx ? ax : cx); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    b=(ax > cx ? ax : cx); 
 {    x=w=v=bx; 
   double  **a,**y,*x,pd;    fw=fv=fx=(*f)(x); 
   double **hess;    for (iter=1;iter<=ITMAX;iter++) { 
   int i, j,jk;      xm=0.5*(a+b); 
   int *indx;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   double hessii(double p[], double delta, int theta, double delti[]);      printf(".");fflush(stdout);
   double hessij(double p[], double delti[], int i, int j);      fprintf(ficlog,".");fflush(ficlog);
   void lubksb(double **a, int npar, int *indx, double b[]) ;  #ifdef DEBUG
   void ludcmp(double **a, int npar, int *indx, double *d) ;      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);
   hess=matrix(1,npar,1,npar);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   #endif
   printf("\nCalculation of the hessian matrix. Wait...\n");      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   for (i=1;i<=npar;i++){        *xmin=x; 
     printf("%d",i);fflush(stdout);        return fx; 
     hess[i][i]=hessii(p,ftolhess,i,delti);      } 
     /*printf(" %f ",p[i]);*/      ftemp=fu;
     /*printf(" %lf ",hess[i][i]);*/      if (fabs(e) > tol1) { 
   }        r=(x-w)*(fx-fv); 
          q=(x-v)*(fx-fw); 
   for (i=1;i<=npar;i++) {        p=(x-v)*q-(x-w)*r; 
     for (j=1;j<=npar;j++)  {        q=2.0*(q-r); 
       if (j>i) {        if (q > 0.0) p = -p; 
         printf(".%d%d",i,j);fflush(stdout);        q=fabs(q); 
         hess[i][j]=hessij(p,delti,i,j);        etemp=e; 
         hess[j][i]=hess[i][j];            e=d; 
         /*printf(" %lf ",hess[i][j]);*/        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       }          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     }        else { 
   }          d=p/q; 
   printf("\n");          u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");            d=SIGN(tol1,xm-x); 
          } 
   a=matrix(1,npar,1,npar);      } else { 
   y=matrix(1,npar,1,npar);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   x=vector(1,npar);      } 
   indx=ivector(1,npar);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   for (i=1;i<=npar;i++)      fu=(*f)(u); 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      if (fu <= fx) { 
   ludcmp(a,npar,indx,&pd);        if (u >= x) a=x; else b=x; 
         SHFT(v,w,x,u) 
   for (j=1;j<=npar;j++) {          SHFT(fv,fw,fx,fu) 
     for (i=1;i<=npar;i++) x[i]=0;          } else { 
     x[j]=1;            if (u < x) a=u; else b=u; 
     lubksb(a,npar,indx,x);            if (fu <= fw || w == x) { 
     for (i=1;i<=npar;i++){              v=w; 
       matcov[i][j]=x[i];              w=u; 
     }              fv=fw; 
   }              fw=fu; 
             } else if (fu <= fv || v == x || v == w) { 
   printf("\n#Hessian matrix#\n");              v=u; 
   for (i=1;i<=npar;i++) {              fv=fu; 
     for (j=1;j<=npar;j++) {            } 
       printf("%.3e ",hess[i][j]);          } 
     }    } 
     printf("\n");    nrerror("Too many iterations in brent"); 
   }    *xmin=x; 
     return fx; 
   /* Recompute Inverse */  } 
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  /****************** mnbrak ***********************/
   ludcmp(a,npar,indx,&pd);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   /*  printf("\n#Hessian matrix recomputed#\n");              double (*func)(double)) 
   { 
   for (j=1;j<=npar;j++) {    double ulim,u,r,q, dum;
     for (i=1;i<=npar;i++) x[i]=0;    double fu; 
     x[j]=1;   
     lubksb(a,npar,indx,x);    *fa=(*func)(*ax); 
     for (i=1;i<=npar;i++){    *fb=(*func)(*bx); 
       y[i][j]=x[i];    if (*fb > *fa) { 
       printf("%.3e ",y[i][j]);      SHFT(dum,*ax,*bx,dum) 
     }        SHFT(dum,*fb,*fa,dum) 
     printf("\n");        } 
   }    *cx=(*bx)+GOLD*(*bx-*ax); 
   */    *fc=(*func)(*cx); 
     while (*fb > *fc) { 
   free_matrix(a,1,npar,1,npar);      r=(*bx-*ax)*(*fb-*fc); 
   free_matrix(y,1,npar,1,npar);      q=(*bx-*cx)*(*fb-*fa); 
   free_vector(x,1,npar);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   free_ivector(indx,1,npar);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   free_matrix(hess,1,npar,1,npar);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if ((*bx-u)*(u-*cx) > 0.0) { 
         fu=(*func)(u); 
 }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         fu=(*func)(u); 
 /*************** hessian matrix ****************/        if (fu < *fc) { 
 double hessii( double x[], double delta, int theta, double delti[])          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
 {            SHFT(*fb,*fc,fu,(*func)(u)) 
   int i;            } 
   int l=1, lmax=20;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   double k1,k2;        u=ulim; 
   double p2[NPARMAX+1];        fu=(*func)(u); 
   double res;      } else { 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        u=(*cx)+GOLD*(*cx-*bx); 
   double fx;        fu=(*func)(u); 
   int k=0,kmax=10;      } 
   double l1;      SHFT(*ax,*bx,*cx,u) 
         SHFT(*fa,*fb,*fc,fu) 
   fx=func(x);        } 
   for (i=1;i<=npar;i++) p2[i]=x[i];  } 
   for(l=0 ; l <=lmax; l++){  
     l1=pow(10,l);  /*************** linmin ************************/
     delts=delt;  
     for(k=1 ; k <kmax; k=k+1){  int ncom; 
       delt = delta*(l1*k);  double *pcom,*xicom;
       p2[theta]=x[theta] +delt;  double (*nrfunc)(double []); 
       k1=func(p2)-fx;   
       p2[theta]=x[theta]-delt;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       k2=func(p2)-fx;  { 
       /*res= (k1-2.0*fx+k2)/delt/delt; */    double brent(double ax, double bx, double cx, 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */                 double (*f)(double), double tol, double *xmin); 
          double f1dim(double x); 
 #ifdef DEBUG    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       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);                double *fc, double (*func)(double)); 
 #endif    int j; 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    double xx,xmin,bx,ax; 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    double fx,fb,fa;
         k=kmax;   
       }    ncom=n; 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    pcom=vector(1,n); 
         k=kmax; l=lmax*10.;    xicom=vector(1,n); 
       }    nrfunc=func; 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    for (j=1;j<=n;j++) { 
         delts=delt;      pcom[j]=p[j]; 
       }      xicom[j]=xi[j]; 
     }    } 
   }    ax=0.0; 
   delti[theta]=delts;    xx=1.0; 
   return res;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
      *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 }  #ifdef DEBUG
     printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 double hessij( double x[], double delti[], int thetai,int thetaj)    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 {  #endif
   int i;    for (j=1;j<=n;j++) { 
   int l=1, l1, lmax=20;      xi[j] *= xmin; 
   double k1,k2,k3,k4,res,fx;      p[j] += xi[j]; 
   double p2[NPARMAX+1];    } 
   int k;    free_vector(xicom,1,n); 
     free_vector(pcom,1,n); 
   fx=func(x);  } 
   for (k=1; k<=2; k++) {  
     for (i=1;i<=npar;i++) p2[i]=x[i];  char *asc_diff_time(long time_sec, char ascdiff[])
     p2[thetai]=x[thetai]+delti[thetai]/k;  {
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    long sec_left, days, hours, minutes;
     k1=func(p2)-fx;    days = (time_sec) / (60*60*24);
      sec_left = (time_sec) % (60*60*24);
     p2[thetai]=x[thetai]+delti[thetai]/k;    hours = (sec_left) / (60*60) ;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    sec_left = (sec_left) %(60*60);
     k2=func(p2)-fx;    minutes = (sec_left) /60;
      sec_left = (sec_left) % (60);
     p2[thetai]=x[thetai]-delti[thetai]/k;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    return ascdiff;
     k3=func(p2)-fx;  }
    
     p2[thetai]=x[thetai]-delti[thetai]/k;  /*************** powell ************************/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     k4=func(p2)-fx;              double (*func)(double [])) 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  { 
 #ifdef DEBUG    void linmin(double p[], double xi[], int n, double *fret, 
     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);                double (*func)(double [])); 
 #endif    int i,ibig,j; 
   }    double del,t,*pt,*ptt,*xit;
   return res;    double fp,fptt;
 }    double *xits;
     int niterf, itmp;
 /************** Inverse of matrix **************/  
 void ludcmp(double **a, int n, int *indx, double *d)    pt=vector(1,n); 
 {    ptt=vector(1,n); 
   int i,imax,j,k;    xit=vector(1,n); 
   double big,dum,sum,temp;    xits=vector(1,n); 
   double *vv;    *fret=(*func)(p); 
      for (j=1;j<=n;j++) pt[j]=p[j]; 
   vv=vector(1,n);    for (*iter=1;;++(*iter)) { 
   *d=1.0;      fp=(*fret); 
   for (i=1;i<=n;i++) {      ibig=0; 
     big=0.0;      del=0.0; 
     for (j=1;j<=n;j++)      last_time=curr_time;
       if ((temp=fabs(a[i][j])) > big) big=temp;      (void) gettimeofday(&curr_time,&tzp);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      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);
     vv[i]=1.0/big;      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);
   }  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
   for (j=1;j<=n;j++) {     for (i=1;i<=n;i++) {
     for (i=1;i<j;i++) {        printf(" %d %.12f",i, p[i]);
       sum=a[i][j];        fprintf(ficlog," %d %.12lf",i, p[i]);
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        fprintf(ficrespow," %.12lf", p[i]);
       a[i][j]=sum;      }
     }      printf("\n");
     big=0.0;      fprintf(ficlog,"\n");
     for (i=j;i<=n;i++) {      fprintf(ficrespow,"\n");fflush(ficrespow);
       sum=a[i][j];      if(*iter <=3){
       for (k=1;k<j;k++)        tm = *localtime(&curr_time.tv_sec);
         sum -= a[i][k]*a[k][j];        strcpy(strcurr,asctime(&tm));
       a[i][j]=sum;  /*       asctime_r(&tm,strcurr); */
       if ( (dum=vv[i]*fabs(sum)) >= big) {        forecast_time=curr_time; 
         big=dum;        itmp = strlen(strcurr);
         imax=i;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
       }          strcurr[itmp-1]='\0';
     }        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     if (j != imax) {        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       for (k=1;k<=n;k++) {        for(niterf=10;niterf<=30;niterf+=10){
         dum=a[imax][k];          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
         a[imax][k]=a[j][k];          tmf = *localtime(&forecast_time.tv_sec);
         a[j][k]=dum;  /*      asctime_r(&tmf,strfor); */
       }          strcpy(strfor,asctime(&tmf));
       *d = -(*d);          itmp = strlen(strfor);
       vv[imax]=vv[j];          if(strfor[itmp-1]=='\n')
     }          strfor[itmp-1]='\0';
     indx[j]=imax;          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);
     if (a[j][j] == 0.0) a[j][j]=TINY;          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);
     if (j != n) {        }
       dum=1.0/(a[j][j]);      }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      for (i=1;i<=n;i++) { 
     }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   }        fptt=(*fret); 
   free_vector(vv,1,n);  /* Doesn't work */  #ifdef DEBUG
 ;        printf("fret=%lf \n",*fret);
 }        fprintf(ficlog,"fret=%lf \n",*fret);
   #endif
 void lubksb(double **a, int n, int *indx, double b[])        printf("%d",i);fflush(stdout);
 {        fprintf(ficlog,"%d",i);fflush(ficlog);
   int i,ii=0,ip,j;        linmin(p,xit,n,fret,func); 
   double sum;        if (fabs(fptt-(*fret)) > del) { 
            del=fabs(fptt-(*fret)); 
   for (i=1;i<=n;i++) {          ibig=i; 
     ip=indx[i];        } 
     sum=b[ip];  #ifdef DEBUG
     b[ip]=b[i];        printf("%d %.12e",i,(*fret));
     if (ii)        fprintf(ficlog,"%d %.12e",i,(*fret));
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        for (j=1;j<=n;j++) {
     else if (sum) ii=i;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     b[i]=sum;          printf(" x(%d)=%.12e",j,xit[j]);
   }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   for (i=n;i>=1;i--) {        }
     sum=b[i];        for(j=1;j<=n;j++) {
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          printf(" p=%.12e",p[j]);
     b[i]=sum/a[i][i];          fprintf(ficlog," p=%.12e",p[j]);
   }        }
 }        printf("\n");
         fprintf(ficlog,"\n");
 /************ Frequencies ********************/  #endif
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2)      } 
 {  /* Some frequencies */      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
    #ifdef DEBUG
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        int k[2],l;
   double ***freq; /* Frequencies */        k[0]=1;
   double *pp;        k[1]=-1;
   double pos, k2, dateintsum=0,k2cpt=0;        printf("Max: %.12e",(*func)(p));
   FILE *ficresp;        fprintf(ficlog,"Max: %.12e",(*func)(p));
   char fileresp[FILENAMELENGTH];        for (j=1;j<=n;j++) {
           printf(" %.12e",p[j]);
   pp=vector(1,nlstate);          fprintf(ficlog," %.12e",p[j]);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        }
   strcpy(fileresp,"p");        printf("\n");
   strcat(fileresp,fileres);        fprintf(ficlog,"\n");
   if((ficresp=fopen(fileresp,"w"))==NULL) {        for(l=0;l<=1;l++) {
     printf("Problem with prevalence resultfile: %s\n", fileresp);          for (j=1;j<=n;j++) {
     exit(0);            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]);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   j1=0;          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   j=cptcoveff;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        }
   #endif
   for(k1=1; k1<=j;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){  
        j1++;        free_vector(xit,1,n); 
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        free_vector(xits,1,n); 
          scanf("%d", i);*/        free_vector(ptt,1,n); 
         for (i=-1; i<=nlstate+ndeath; i++)          free_vector(pt,1,n); 
          for (jk=-1; jk<=nlstate+ndeath; jk++)          return; 
            for(m=agemin; m <= agemax+3; m++)      } 
              freq[i][jk][m]=0;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
         dateintsum=0;        ptt[j]=2.0*p[j]-pt[j]; 
         k2cpt=0;        xit[j]=p[j]-pt[j]; 
        for (i=1; i<=imx; i++) {        pt[j]=p[j]; 
          bool=1;      } 
          if  (cptcovn>0) {      fptt=(*func)(ptt); 
            for (z1=1; z1<=cptcoveff; z1++)      if (fptt < fp) { 
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
                bool=0;        if (t < 0.0) { 
          }          linmin(p,xit,n,fret,func); 
          if (bool==1) {          for (j=1;j<=n;j++) { 
            for(m=firstpass; m<=lastpass; m++){            xi[j][ibig]=xi[j][n]; 
              k2=anint[m][i]+(mint[m][i]/12.);            xi[j][n]=xit[j]; 
              if ((k2>=dateprev1) && (k2<=dateprev2)) {          }
                if(agev[m][i]==0) agev[m][i]=agemax+1;  #ifdef DEBUG
                if(agev[m][i]==1) agev[m][i]=agemax+2;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          for(j=1;j<=n;j++){
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {            printf(" %.12e",xit[j]);
                  dateintsum=dateintsum+k2;            fprintf(ficlog," %.12e",xit[j]);
                  k2cpt++;          }
                }          printf("\n");
           fprintf(ficlog,"\n");
              }  #endif
            }        }
          }      } 
        }    } 
         if  (cptcovn>0) {  } 
          fprintf(ficresp, "\n#********** Variable ");  
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  /**** Prevalence limit (stable or period prevalence)  ****************/
        fprintf(ficresp, "**********\n#");  
         }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
        for(i=1; i<=nlstate;i++)  {
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
        fprintf(ficresp, "\n");       matrix by transitions matrix until convergence is reached */
          
   for(i=(int)agemin; i <= (int)agemax+3; i++){    int i, ii,j,k;
     if(i==(int)agemax+3)    double min, max, maxmin, maxmax,sumnew=0.;
       printf("Total");    double **matprod2();
     else    double **out, cov[NCOVMAX+1], **pmij();
       printf("Age %d", i);    double **newm;
     for(jk=1; jk <=nlstate ; jk++){    double agefin, delaymax=50 ; /* Max number of years to converge */
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  
         pp[jk] += freq[jk][m][i];    for (ii=1;ii<=nlstate+ndeath;ii++)
     }      for (j=1;j<=nlstate+ndeath;j++){
     for(jk=1; jk <=nlstate ; jk++){        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(m=-1, pos=0; m <=0 ; m++)      }
         pos += freq[jk][m][i];  
       if(pp[jk]>=1.e-10)     cov[1]=1.;
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);   
       else   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     }      newm=savm;
       /* Covariates have to be included here again */
      for(jk=1; jk <=nlstate ; jk++){      cov[2]=agefin;
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      
         pp[jk] += freq[jk][m][i];      for (k=1; k<=cptcovn;k++) {
      }        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         /*        printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
     for(jk=1,pos=0; jk <=nlstate ; jk++)      }
       pos += pp[jk];      for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for(jk=1; jk <=nlstate ; jk++){      for (k=1; k<=cptcovprod;k++)
       if(pos>=1.e-5)        cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      
       else      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       if( i <= (int) agemax){      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
         if(pos>=1.e-5){      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      
           probs[i][jk][j1]= pp[jk]/pos;      savm=oldm;
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/      oldm=newm;
         }      maxmax=0.;
       else      for(j=1;j<=nlstate;j++){
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        min=1.;
       }        max=0.;
     }        for(i=1; i<=nlstate; i++) {
     for(jk=-1; jk <=nlstate+ndeath; jk++)          sumnew=0;
       for(m=-1; m <=nlstate+ndeath; m++)          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          prlim[i][j]= newm[i][j]/(1-sumnew);
     if(i <= (int) agemax)          max=FMAX(max,prlim[i][j]);
       fprintf(ficresp,"\n");          min=FMIN(min,prlim[i][j]);
     printf("\n");        }
     }        maxmin=max-min;
     }        maxmax=FMAX(maxmax,maxmin);
  }      }
   dateintmean=dateintsum/k2cpt;      if(maxmax < ftolpl){
          return prlim;
   fclose(ficresp);      }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    }
   free_vector(pp,1,nlstate);  }
   
   /* End of Freq */  /*************** transition probabilities ***************/ 
 }  
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 /************ Prevalence ********************/  {
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)    /* According to parameters values stored in x and the covariate's values stored in cov,
 {  /* Some frequencies */       computes the probability to be observed in state j being in state i by appying the
         model to the ncovmodel covariates (including constant and age).
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
   double ***freq; /* Frequencies */       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
   double *pp;       ncth covariate in the global vector x is given by the formula:
   double pos, k2;       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
        j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
   pp=vector(1,nlstate);       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
         Outputs ps[i][j] the probability to be observed in j being in j according to
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
   j1=0;    */
      double s1, lnpijopii;
   j=cptcoveff;    /*double t34;*/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    int i,j,j1, nc, ii, jj;
    
  for(k1=1; k1<=j;k1++){      for(i=1; i<= nlstate; i++){
     for(i1=1; i1<=ncodemax[k1];i1++){        for(j=1; j<i;j++){
       j1++;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
              /*lnpijopii += param[i][j][nc]*cov[nc];*/
       for (i=-1; i<=nlstate+ndeath; i++)              lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
         for (jk=-1; jk<=nlstate+ndeath; jk++)    /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
           for(m=agemin; m <= agemax+3; m++)          }
             freq[i][jk][m]=0;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
        /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       for (i=1; i<=imx; i++) {        }
         bool=1;        for(j=i+1; j<=nlstate+ndeath;j++){
         if  (cptcovn>0) {          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
           for (z1=1; z1<=cptcoveff; z1++)            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
               bool=0;  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
         }          }
         if (bool==1) {          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
           for(m=firstpass; m<=lastpass; m++){        }
             k2=anint[m][i]+(mint[m][i]/12.);      }
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      
               if(agev[m][i]==0) agev[m][i]=agemax+1;      for(i=1; i<= nlstate; i++){
               if(agev[m][i]==1) agev[m][i]=agemax+2;        s1=0;
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        for(j=1; j<i; j++){
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];            s1+=exp(ps[i][j]); /* In fact sums pij/pii */
             }          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           }        }
         }        for(j=i+1; j<=nlstate+ndeath; j++){
       }          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
                /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
         for(i=(int)agemin; i <= (int)agemax+3; i++){        }
           for(jk=1; jk <=nlstate ; jk++){        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        ps[i][i]=1./(s1+1.);
               pp[jk] += freq[jk][m][i];        /* Computing other pijs */
           }        for(j=1; j<i; j++)
           for(jk=1; jk <=nlstate ; jk++){          ps[i][j]= exp(ps[i][j])*ps[i][i];
             for(m=-1, pos=0; m <=0 ; m++)        for(j=i+1; j<=nlstate+ndeath; j++)
             pos += freq[jk][m][i];          ps[i][j]= exp(ps[i][j])*ps[i][i];
         }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
              } /* end i */
          for(jk=1; jk <=nlstate ; jk++){      
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
              pp[jk] += freq[jk][m][i];        for(jj=1; jj<= nlstate+ndeath; jj++){
          }          ps[ii][jj]=0;
                    ps[ii][ii]=1;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        }
       }
          for(jk=1; jk <=nlstate ; jk++){                
            if( i <= (int) agemax){  
              if(pos>=1.e-5){  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
                probs[i][jk][j1]= pp[jk]/pos;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
              }  /*         printf("ddd %lf ",ps[ii][jj]); */
            }  /*       } */
          }  /*       printf("\n "); */
            /*        } */
         }  /*        printf("\n ");printf("%lf ",cov[2]); */
     }         /*
   }        for(i=1; i<= npar; i++) printf("%f ",x[i]);
          goto end;*/
        return ps;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  }
   free_vector(pp,1,nlstate);  
    /**************** Product of 2 matrices ******************/
 }  /* End of Freq */  
   double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
 /************* Waves Concatenation ***************/  {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
 {    /* in, b, out are matrice of pointers which should have been initialized 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.       before: only the contents of out is modified. The function returns
      Death is a valid wave (if date is known).       a pointer to pointers identical to out */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    long i, j, k;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    for(i=nrl; i<= nrh; i++)
      and mw[mi+1][i]. dh depends on stepm.      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];
   int i, mi, m;  
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    return out;
      double sum=0., jmean=0.;*/  }
   
   int j, k=0,jk, ju, jl;  
   double sum=0.;  /************* Higher Matrix Product ***************/
   jmin=1e+5;  
   jmax=-1;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   jmean=0.;  {
   for(i=1; i<=imx; i++){    /* Computes the transition matrix starting at age 'age' over 
     mi=0;       'nhstepm*hstepm*stepm' months (i.e. until
     m=firstpass;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     while(s[m][i] <= nlstate){       nhstepm*hstepm matrices. 
       if(s[m][i]>=1)       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         mw[++mi][i]=m;       (typically every 2 years instead of every month which is too big 
       if(m >=lastpass)       for the memory).
         break;       Model is determined by parameters x and covariates have to be 
       else       included manually here. 
         m++;  
     }/* end while */       */
     if (s[m][i] > nlstate){  
       mi++;     /* Death is another wave */    int i, j, d, h, k;
       /* if(mi==0)  never been interviewed correctly before death */    double **out, cov[NCOVMAX+1];
          /* Only death is a correct wave */    double **newm;
       mw[mi][i]=m;  
     }    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
     wav[i]=mi;      for (j=1;j<=nlstate+ndeath;j++){
     if(mi==0)        oldm[i][j]=(i==j ? 1.0 : 0.0);
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        po[i][j][0]=(i==j ? 1.0 : 0.0);
   }      }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for(i=1; i<=imx; i++){    for(h=1; h <=nhstepm; h++){
     for(mi=1; mi<wav[i];mi++){      for(d=1; d <=hstepm; d++){
       if (stepm <=0)        newm=savm;
         dh[mi][i]=1;        /* Covariates have to be included here again */
       else{        cov[1]=1.;
         if (s[mw[mi+1][i]][i] > nlstate) {        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
           if (agedc[i] < 2*AGESUP) {        for (k=1; k<=cptcovn;k++) 
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           if(j==0) j=1;  /* Survives at least one month after exam */        for (k=1; k<=cptcovage;k++)
           k=k+1;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           if (j >= jmax) jmax=j;        for (k=1; k<=cptcovprod;k++)
           if (j <= jmin) jmin=j;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           sum=sum+j;  
           /* if (j<10) printf("j=%d num=%d ",j,i); */  
           }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         else{        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));                     pmij(pmmij,cov,ncovmodel,x,nlstate));
           k=k+1;        savm=oldm;
           if (j >= jmax) jmax=j;        oldm=newm;
           else if (j <= jmin)jmin=j;      }
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */      for(i=1; i<=nlstate+ndeath; i++)
           sum=sum+j;        for(j=1;j<=nlstate+ndeath;j++) {
         }          po[i][j][h]=newm[i][j];
         jk= j/stepm;          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
         jl= j -jk*stepm;        }
         ju= j -(jk+1)*stepm;      /*printf("h=%d ",h);*/
         if(jl <= -ju)    } /* end h */
           dh[mi][i]=jk;  /*     printf("\n H=%d \n",h); */
         else    return po;
           dh[mi][i]=jk+1;  }
         if(dh[mi][i]==0)  
           dh[mi][i]=1; /* At least one step */  
       }  /*************** log-likelihood *************/
     }  double func( double *x)
   }  {
   jmean=sum/k;    int i, ii, j, k, mi, d, kk;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
  }    double **out;
 /*********** Tricode ****************************/    double sw; /* Sum of weights */
 void tricode(int *Tvar, int **nbcode, int imx)    double lli; /* Individual log likelihood */
 {    int s1, s2;
   int Ndum[20],ij=1, k, j, i;    double bbh, survp;
   int cptcode=0;    long ipmx;
   cptcoveff=0;    /*extern weight */
      /* We are differentiating ll according to initial status */
   for (k=0; k<19; k++) Ndum[k]=0;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   for (k=1; k<=7; k++) ncodemax[k]=0;    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    */
     for (i=1; i<=imx; i++) {    cov[1]=1.;
       ij=(int)(covar[Tvar[j]][i]);  
       Ndum[ij]++;    for(k=1; k<=nlstate; k++) ll[k]=0.;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  
       if (ij > cptcode) cptcode=ij;    if(mle==1){
     }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         /* Computes the values of the ncovmodel covariates of the model
     for (i=0; i<=cptcode; i++) {           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
       if(Ndum[i]!=0) ncodemax[j]++;           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
     }           to be observed in j being in i according to the model.
     ij=1;         */
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
     for (i=1; i<=ncodemax[j]; i++) {           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
       for (k=0; k<=19; k++) {           has been calculated etc */
         if (Ndum[k] != 0) {        for(mi=1; mi<= wav[i]-1; mi++){
           nbcode[Tvar[j]][ij]=k;          for (ii=1;ii<=nlstate+ndeath;ii++)
           ij++;            for (j=1;j<=nlstate+ndeath;j++){
         }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         if (ij > ncodemax[j]) break;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              }
     }          for(d=0; d<dh[mi][i]; d++){
   }              newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
  for (k=0; k<19; k++) Ndum[k]=0;            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
  for (i=1; i<=ncovmodel-2; i++) {            }
       ij=Tvar[i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       Ndum[ij]++;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
             oldm=newm;
  ij=1;          } /* end mult */
  for (i=1; i<=10; i++) {        
    if((Ndum[i]!=0) && (i<=ncov)){          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
      Tvaraff[ij]=i;          /* But now since version 0.9 we anticipate for bias at large stepm.
      ij++;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
    }           * (in months) between two waves is not a multiple of stepm, we rounded to 
  }           * the nearest (and in case of equal distance, to the lowest) interval but now
             * we keep into memory the bias bh[mi][i] and also the previous matrix product
     cptcoveff=ij-1;           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
 }           * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is negative or even beyond if bh is positive. bh varies
 /*********** Health Expectancies ****************/           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)           * For stepm > 1 the results are less biased than in previous versions. 
 {           */
   /* Health expectancies */          s1=s[mw[mi][i]][i];
   int i, j, nhstepm, hstepm, h;          s2=s[mw[mi+1][i]][i];
   double age, agelim,hf;          bbh=(double)bh[mi][i]/(double)stepm; 
   double ***p3mat;          /* bias bh is positive if real duration
             * is higher than the multiple of stepm and negative otherwise.
   fprintf(ficreseij,"# Health expectancies\n");           */
   fprintf(ficreseij,"# Age");          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   for(i=1; i<=nlstate;i++)          if( s2 > nlstate){ 
     for(j=1; j<=nlstate;j++)            /* i.e. if s2 is a death state and if the date of death is known 
       fprintf(ficreseij," %1d-%1d",i,j);               then the contribution to the likelihood is the probability to 
   fprintf(ficreseij,"\n");               die between last step unit time and current  step unit time, 
                which is also equal to probability to die before dh 
   hstepm=1*YEARM; /*  Every j years of age (in month) */               minus probability to die before dh-stepm . 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
   agelim=AGESUP;          health state: the date of the interview describes the actual state
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          and not the date of a change in health state. The former idea was
     /* nhstepm age range expressed in number of stepm */          to consider that at each interview the state was recorded
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);          (healthy, disable or death) and IMaCh was corrected; but when we
     /* Typically if 20 years = 20*12/6=40 stepm */          introduced the exact date of death then we should have modified
     if (stepm >= YEARM) hstepm=1;          the contribution of an exact death to the likelihood. This new
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */          contribution is smaller and very dependent of the step unit
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          stepm. It is no more the probability to die between last interview
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          and month of death but the probability to survive from last
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          interview up to one month before death multiplied by the
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            probability to die within a month. Thanks to Chris
           Jackson for correcting this bug.  Former versions increased
           mortality artificially. The bad side is that we add another loop
     for(i=1; i<=nlstate;i++)          which slows down the processing. The difference can be up to 10%
       for(j=1; j<=nlstate;j++)          lower mortality.
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){            */
           eij[i][j][(int)age] +=p3mat[i][j][h];            lli=log(out[s1][s2] - savm[s1][s2]);
         }  
      
     hf=1;          } else if  (s2==-2) {
     if (stepm >= YEARM) hf=stepm/YEARM;            for (j=1,survp=0. ; j<=nlstate; j++) 
     fprintf(ficreseij,"%.0f",age );              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     for(i=1; i<=nlstate;i++)            /*survp += out[s1][j]; */
       for(j=1; j<=nlstate;j++){            lli= log(survp);
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          }
       }          
     fprintf(ficreseij,"\n");          else if  (s2==-4) { 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for (j=3,survp=0. ; j<=nlstate; j++)  
   }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 }            lli= log(survp); 
           } 
 /************ Variance ******************/  
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)          else if  (s2==-5) { 
 {            for (j=1,survp=0. ; j<=2; j++)  
   /* Variance of health expectancies */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            lli= log(survp); 
   double **newm;          } 
   double **dnewm,**doldm;          
   int i, j, nhstepm, hstepm, h;          else{
   int k, cptcode;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double *xp;            /*  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 */
   double **gp, **gm;          } 
   double ***gradg, ***trgradg;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double ***p3mat;          /*if(lli ==000.0)*/
   double age,agelim;          /*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); */
   int theta;          ipmx +=1;
           sw += weight[i];
    fprintf(ficresvij,"# Covariances of life expectancies\n");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   fprintf(ficresvij,"# Age");        } /* end of wave */
   for(i=1; i<=nlstate;i++)      } /* end of individual */
     for(j=1; j<=nlstate;j++)    }  else if(mle==2){
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   fprintf(ficresvij,"\n");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   xp=vector(1,npar);          for (ii=1;ii<=nlstate+ndeath;ii++)
   dnewm=matrix(1,nlstate,1,npar);            for (j=1;j<=nlstate+ndeath;j++){
   doldm=matrix(1,nlstate,1,nlstate);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
   hstepm=1*YEARM; /* Every year of age */            }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          for(d=0; d<=dh[mi][i]; d++){
   agelim = AGESUP;            newm=savm;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            for (kk=1; kk<=cptcovage;kk++) {
     if (stepm >= YEARM) hstepm=1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     gp=matrix(0,nhstepm,1,nlstate);            savm=oldm;
     gm=matrix(0,nhstepm,1,nlstate);            oldm=newm;
           } /* end mult */
     for(theta=1; theta <=npar; theta++){        
       for(i=1; i<=npar; i++){ /* Computes gradient */          s1=s[mw[mi][i]][i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          s2=s[mw[mi+1][i]][i];
       }          bbh=(double)bh[mi][i]/(double)stepm; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            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 */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          ipmx +=1;
           sw += weight[i];
       if (popbased==1) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for(i=1; i<=nlstate;i++)        } /* end of wave */
           prlim[i][i]=probs[(int)age][i][ij];      } /* end of individual */
       }    }  else if(mle==3){  /* exponential inter-extrapolation */
            for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(j=1; j<= nlstate; j++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(h=0; h<=nhstepm; h++){        for(mi=1; mi<= wav[i]-1; mi++){
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          for (ii=1;ii<=nlstate+ndeath;ii++)
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            for (j=1;j<=nlstate+ndeath;j++){
         }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                }
       for(i=1; i<=npar; i++) /* Computes gradient */          for(d=0; d<dh[mi][i]; d++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            newm=savm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       if (popbased==1) {            }
         for(i=1; i<=nlstate;i++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           prlim[i][i]=probs[(int)age][i][ij];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
             oldm=newm;
       for(j=1; j<= nlstate; j++){          } /* end mult */
         for(h=0; h<=nhstepm; h++){        
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          s1=s[mw[mi][i]][i];
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          s2=s[mw[mi+1][i]][i];
         }          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 */
           ipmx +=1;
       for(j=1; j<= nlstate; j++)          sw += weight[i];
         for(h=0; h<=nhstepm; h++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        } /* end of wave */
         }      } /* end of individual */
     } /* End theta */    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
     for(h=0; h<=nhstepm; h++)          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(j=1; j<=nlstate;j++)            for (j=1;j<=nlstate+ndeath;j++){
         for(theta=1; theta <=npar; theta++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           trgradg[h][j][theta]=gradg[h][theta][j];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
     for(i=1;i<=nlstate;i++)          for(d=0; d<dh[mi][i]; d++){
       for(j=1;j<=nlstate;j++)            newm=savm;
         vareij[i][j][(int)age] =0.;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(h=0;h<=nhstepm;h++){            for (kk=1; kk<=cptcovage;kk++) {
       for(k=0;k<=nhstepm;k++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);            }
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          
         for(i=1;i<=nlstate;i++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           for(j=1;j<=nlstate;j++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             vareij[i][j][(int)age] += doldm[i][j];            savm=oldm;
       }            oldm=newm;
     }          } /* end mult */
     h=1;        
     if (stepm >= YEARM) h=stepm/YEARM;          s1=s[mw[mi][i]][i];
     fprintf(ficresvij,"%.0f ",age );          s2=s[mw[mi+1][i]][i];
     for(i=1; i<=nlstate;i++)          if( s2 > nlstate){ 
       for(j=1; j<=nlstate;j++){            lli=log(out[s1][s2] - savm[s1][s2]);
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);          }else{
       }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     fprintf(ficresvij,"\n");          }
     free_matrix(gp,0,nhstepm,1,nlstate);          ipmx +=1;
     free_matrix(gm,0,nhstepm,1,nlstate);          sw += weight[i];
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  /*      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]); */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        } /* end of wave */
   } /* End age */      } /* end of individual */
      }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   free_vector(xp,1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_matrix(doldm,1,nlstate,1,npar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   free_matrix(dnewm,1,nlstate,1,nlstate);        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);
 /************ Variance of prevlim ******************/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 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)            }
 {          for(d=0; d<dh[mi][i]; d++){
   /* Variance of prevalence limit */            newm=savm;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double **newm;            for (kk=1; kk<=cptcovage;kk++) {
   double **dnewm,**doldm;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int i, j, nhstepm, hstepm;            }
   int k, cptcode;          
   double *xp;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double *gp, *gm;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double **gradg, **trgradg;            savm=oldm;
   double age,agelim;            oldm=newm;
   int theta;          } /* end mult */
            
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          s1=s[mw[mi][i]][i];
   fprintf(ficresvpl,"# Age");          s2=s[mw[mi+1][i]][i];
   for(i=1; i<=nlstate;i++)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       fprintf(ficresvpl," %1d-%1d",i,i);          ipmx +=1;
   fprintf(ficresvpl,"\n");          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   xp=vector(1,npar);          /*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]);*/
   dnewm=matrix(1,nlstate,1,npar);        } /* end of wave */
   doldm=matrix(1,nlstate,1,nlstate);      } /* end of individual */
      } /* End of if */
   hstepm=1*YEARM; /* Every year of age */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   agelim = AGESUP;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    return -l;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  }
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  /*************** log-likelihood *************/
     gradg=matrix(1,npar,1,nlstate);  double funcone( double *x)
     gp=vector(1,nlstate);  {
     gm=vector(1,nlstate);    /* Same as likeli but slower because of a lot of printf and if */
     int i, ii, j, k, mi, d, kk;
     for(theta=1; theta <=npar; theta++){    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
       for(i=1; i<=npar; i++){ /* Computes gradient */    double **out;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double lli; /* Individual log likelihood */
       }    double llt;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int s1, s2;
       for(i=1;i<=nlstate;i++)    double bbh, survp;
         gp[i] = prlim[i][i];    /*extern weight */
        /* We are differentiating ll according to initial status */
       for(i=1; i<=npar; i++) /* Computes gradient */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    /*for(i=1;i<imx;i++) 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      printf(" %d\n",s[4][i]);
       for(i=1;i<=nlstate;i++)    */
         gm[i] = prlim[i][i];    cov[1]=1.;
   
       for(i=1;i<=nlstate;i++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  
     } /* End theta */    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     trgradg =matrix(1,nlstate,1,npar);      for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)
     for(j=1; j<=nlstate;j++)          for (j=1;j<=nlstate+ndeath;j++){
       for(theta=1; theta <=npar; theta++)            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         trgradg[j][theta]=gradg[theta][j];            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
     for(i=1;i<=nlstate;i++)        for(d=0; d<dh[mi][i]; d++){
       varpl[i][(int)age] =0.;          newm=savm;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          for (kk=1; kk<=cptcovage;kk++) {
     for(i=1;i<=nlstate;i++)            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     fprintf(ficresvpl,"%.0f ",age );                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(i=1; i<=nlstate;i++)          savm=oldm;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          oldm=newm;
     fprintf(ficresvpl,"\n");        } /* end mult */
     free_vector(gp,1,nlstate);        
     free_vector(gm,1,nlstate);        s1=s[mw[mi][i]][i];
     free_matrix(gradg,1,npar,1,nlstate);        s2=s[mw[mi+1][i]][i];
     free_matrix(trgradg,1,nlstate,1,npar);        bbh=(double)bh[mi][i]/(double)stepm; 
   } /* End age */        /* bias is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.
   free_vector(xp,1,npar);         */
   free_matrix(doldm,1,nlstate,1,npar);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   free_matrix(dnewm,1,nlstate,1,nlstate);          lli=log(out[s1][s2] - savm[s1][s2]);
         } else if  (s2==-2) {
 }          for (j=1,survp=0. ; j<=nlstate; j++) 
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 /************ Variance of one-step probabilities  ******************/          lli= log(survp);
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        }else if (mle==1){
 {          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   int i, j;        } else if(mle==2){
   int k=0, cptcode;          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 */
   double **dnewm,**doldm;        } else if(mle==3){  /* exponential inter-extrapolation */
   double *xp;          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 */
   double *gp, *gm;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   double **gradg, **trgradg;          lli=log(out[s1][s2]); /* Original formula */
   double age,agelim, cov[NCOVMAX];        } else{  /* mle=0 back to 1 */
   int theta;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   char fileresprob[FILENAMELENGTH];          /*lli=log(out[s1][s2]); */ /* Original formula */
         } /* End of if */
   strcpy(fileresprob,"prob");        ipmx +=1;
   strcat(fileresprob,fileres);        sw += weight[i];
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     printf("Problem with resultfile: %s\n", fileresprob);        /*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(globpr){
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          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],
   xp=vector(1,npar);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));            llt +=ll[k]*gipmx/gsw;
              fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   cov[1]=1;          }
   for (age=bage; age<=fage; age ++){          fprintf(ficresilk," %10.6f\n", -llt);
     cov[2]=age;        }
     gradg=matrix(1,npar,1,9);      } /* end of wave */
     trgradg=matrix(1,9,1,npar);    } /* end of individual */
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    /* 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++){    if(globpr==0){ /* First time we count the contributions and weights */
       for(i=1; i<=npar; i++)      gipmx=ipmx;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      gsw=sw;
          }
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    return -l;
      }
       k=0;  
       for(i=1; i<= (nlstate+ndeath); i++){  
         for(j=1; j<=(nlstate+ndeath);j++){  /*************** function likelione ***********/
            k=k+1;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
           gp[k]=pmmij[i][j];  {
         }    /* This routine should help understanding what is done with 
       }       the selection of individuals/waves and
        to check the exact contribution to the likelihood.
       for(i=1; i<=npar; i++)       Plotting could be done.
         xp[i] = x[i] - (i==theta ?delti[theta]:0);     */
        int k;
   
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    if(*globpri !=0){ /* Just counts and sums, no printings */
       k=0;      strcpy(fileresilk,"ilk"); 
       for(i=1; i<=(nlstate+ndeath); i++){      strcat(fileresilk,fileres);
         for(j=1; j<=(nlstate+ndeath);j++){      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
           k=k+1;        printf("Problem with resultfile: %s\n", fileresilk);
           gm[k]=pmmij[i][j];        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
         }      }
       }      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
            fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); 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]); */
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        for(k=1; k<=nlstate; k++) 
     }        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    }
       for(theta=1; theta <=npar; theta++)  
       trgradg[j][theta]=gradg[theta][j];    *fretone=(*funcone)(p);
      if(*globpri !=0){
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      fclose(ficresilk);
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fflush(fichtm); 
      pmij(pmmij,cov,ncovmodel,x,nlstate);    } 
     return;
      k=0;  }
      for(i=1; i<=(nlstate+ndeath); i++){  
        for(j=1; j<=(nlstate+ndeath);j++){  
          k=k+1;  /*********** Maximum Likelihood Estimation ***************/
          gm[k]=pmmij[i][j];  
         }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
      }  {
          int i,j, iter;
      /*printf("\n%d ",(int)age);    double **xi;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    double fret;
            double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    xi=matrix(1,npar,1,npar);
      }*/    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
   fprintf(ficresprob,"\n%d ",(int)age);        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    strcpy(filerespow,"pow"); 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    strcat(filerespow,fileres);
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    }
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    for (i=1;i<=nlstate;i++)
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      for(j=1;j<=nlstate+ndeath;j++)
 }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
  free_vector(xp,1,npar);    fprintf(ficrespow,"\n");
 fclose(ficresprob);  
  exit(0);    powell(p,xi,npar,ftol,&iter,&fret,func);
 }  
     free_matrix(xi,1,npar,1,npar);
 /***********************************************/    fclose(ficrespow);
 /**************** Main Program *****************/    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
 /***********************************************/    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
 int main(int argc, char *argv[])  
 {  }
   
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  /**** Computes Hessian and covariance matrix ***/
   double agedeb, agefin,hf;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   double agemin=1.e20, agemax=-1.e20;  {
     double  **a,**y,*x,pd;
   double fret;    double **hess;
   double **xi,tmp,delta;    int i, j,jk;
     int *indx;
   double dum; /* Dummy variable */  
   double ***p3mat;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   int *indx;    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   char line[MAXLINE], linepar[MAXLINE];    void lubksb(double **a, int npar, int *indx, double b[]) ;
   char title[MAXLINE];    void ludcmp(double **a, int npar, int *indx, double *d) ;
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    double gompertz(double p[]);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    hess=matrix(1,npar,1,npar);
    
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];;    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   char filerest[FILENAMELENGTH];    for (i=1;i<=npar;i++){
   char fileregp[FILENAMELENGTH];      printf("%d",i);fflush(stdout);
   char popfile[FILENAMELENGTH];      fprintf(ficlog,"%d",i);fflush(ficlog);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];     
   int firstobs=1, lastobs=10;       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   int sdeb, sfin; /* Status at beginning and end */      
   int c,  h , cpt,l;      /*  printf(" %f ",p[i]);
   int ju,jl, mi;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    }
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    
   int mobilav=0,popforecast=0;    for (i=1;i<=npar;i++) {
   int hstepm, nhstepm;      for (j=1;j<=npar;j++)  {
   int *popage;/*boolprev=0 if date and zero if wave*/        if (j>i) { 
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;          printf(".%d%d",i,j);fflush(stdout);
           fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   double bage, fage, age, agelim, agebase;          hess[i][j]=hessij(p,delti,i,j,func,npar);
   double ftolpl=FTOL;          
   double **prlim;          hess[j][i]=hess[i][j];    
   double *severity;          /*printf(" %lf ",hess[i][j]);*/
   double ***param; /* Matrix of parameters */        }
   double  *p;      }
   double **matcov; /* Matrix of covariance */    }
   double ***delti3; /* Scale */    printf("\n");
   double *delti; /* Scale */    fprintf(ficlog,"\n");
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   double *epj, vepp;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   double kk1, kk2;    
   double *popeffectif,*popcount;    a=matrix(1,npar,1,npar);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;    y=matrix(1,npar,1,npar);
   double yp,yp1,yp2;    x=vector(1,npar);
     indx=ivector(1,npar);
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";    for (i=1;i<=npar;i++)
   char *alph[]={"a","a","b","c","d","e"}, str[4];      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     ludcmp(a,npar,indx,&pd);
   
   char z[1]="c", occ;    for (j=1;j<=npar;j++) {
 #include <sys/time.h>      for (i=1;i<=npar;i++) x[i]=0;
 #include <time.h>      x[j]=1;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      lubksb(a,npar,indx,x);
        for (i=1;i<=npar;i++){ 
   /* long total_usecs;        matcov[i][j]=x[i];
   struct timeval start_time, end_time;      }
      }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  
     printf("\n#Hessian matrix#\n");
     fprintf(ficlog,"\n#Hessian matrix#\n");
   printf("\n%s",version);    for (i=1;i<=npar;i++) { 
   if(argc <=1){      for (j=1;j<=npar;j++) { 
     printf("\nEnter the parameter file name: ");        printf("%.3e ",hess[i][j]);
     scanf("%s",pathtot);        fprintf(ficlog,"%.3e ",hess[i][j]);
   }      }
   else{      printf("\n");
     strcpy(pathtot,argv[1]);      fprintf(ficlog,"\n");
   }    }
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/  
   /*cygwin_split_path(pathtot,path,optionfile);    /* Recompute Inverse */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    for (i=1;i<=npar;i++)
   /* cutv(path,optionfile,pathtot,'\\');*/      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);  
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    /*  printf("\n#Hessian matrix recomputed#\n");
   chdir(path);  
   replace(pathc,path);    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
 /*-------- arguments in the command line --------*/      x[j]=1;
       lubksb(a,npar,indx,x);
   strcpy(fileres,"r");      for (i=1;i<=npar;i++){ 
   strcat(fileres, optionfilefiname);        y[i][j]=x[i];
   strcat(fileres,".txt");    /* Other files have txt extension */        printf("%.3e ",y[i][j]);
         fprintf(ficlog,"%.3e ",y[i][j]);
   /*---------arguments file --------*/      }
       printf("\n");
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      fprintf(ficlog,"\n");
     printf("Problem with optionfile %s\n",optionfile);    }
     goto end;    */
   }  
     free_matrix(a,1,npar,1,npar);
   strcpy(filereso,"o");    free_matrix(y,1,npar,1,npar);
   strcat(filereso,fileres);    free_vector(x,1,npar);
   if((ficparo=fopen(filereso,"w"))==NULL) {    free_ivector(indx,1,npar);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    free_matrix(hess,1,npar,1,npar);
   }  
   
   /* Reads comments: lines beginning with '#' */  }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  /*************** hessian matrix ****************/
     fgets(line, MAXLINE, ficpar);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     puts(line);  {
     fputs(line,ficparo);    int i;
   }    int l=1, lmax=20;
   ungetc(c,ficpar);    double k1,k2;
     double p2[MAXPARM+1]; /* identical to x */
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    double res;
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    double fx;
 while((c=getc(ficpar))=='#' && c!= EOF){    int k=0,kmax=10;
     ungetc(c,ficpar);    double l1;
     fgets(line, MAXLINE, ficpar);  
     puts(line);    fx=func(x);
     fputs(line,ficparo);    for (i=1;i<=npar;i++) p2[i]=x[i];
   }    for(l=0 ; l <=lmax; l++){
   ungetc(c,ficpar);      l1=pow(10,l);
        delts=delt;
          for(k=1 ; k <kmax; k=k+1){
   covar=matrix(0,NCOVMAX,1,n);        delt = delta*(l1*k);
   cptcovn=0;        p2[theta]=x[theta] +delt;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;        k1=func(p2)-fx;
         p2[theta]=x[theta]-delt;
   ncovmodel=2+cptcovn;        k2=func(p2)-fx;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        /*res= (k1-2.0*fx+k2)/delt/delt; */
          res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   /* Read guess parameters */        
   /* Reads comments: lines beginning with '#' */  #ifdef DEBUGHESS
   while((c=getc(ficpar))=='#' && c!= EOF){        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);
     ungetc(c,ficpar);        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);
     fgets(line, MAXLINE, ficpar);  #endif
     puts(line);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     fputs(line,ficparo);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   }          k=kmax;
   ungetc(c,ficpar);        }
          else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          k=kmax; l=lmax*10.;
     for(i=1; i <=nlstate; i++)        }
     for(j=1; j <=nlstate+ndeath-1; j++){        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       fscanf(ficpar,"%1d%1d",&i1,&j1);          delts=delt;
       fprintf(ficparo,"%1d%1d",i1,j1);        }
       printf("%1d%1d",i,j);      }
       for(k=1; k<=ncovmodel;k++){    }
         fscanf(ficpar," %lf",&param[i][j][k]);    delti[theta]=delts;
         printf(" %lf",param[i][j][k]);    return res; 
         fprintf(ficparo," %lf",param[i][j][k]);    
       }  }
       fscanf(ficpar,"\n");  
       printf("\n");  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
       fprintf(ficparo,"\n");  {
     }    int i;
      int l=1, l1, lmax=20;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    double k1,k2,k3,k4,res,fx;
     double p2[MAXPARM+1];
   p=param[1][1];    int k;
    
   /* Reads comments: lines beginning with '#' */    fx=func(x);
   while((c=getc(ficpar))=='#' && c!= EOF){    for (k=1; k<=2; k++) {
     ungetc(c,ficpar);      for (i=1;i<=npar;i++) p2[i]=x[i];
     fgets(line, MAXLINE, ficpar);      p2[thetai]=x[thetai]+delti[thetai]/k;
     puts(line);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     fputs(line,ficparo);      k1=func(p2)-fx;
   }    
   ungetc(c,ficpar);      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      k2=func(p2)-fx;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    
   for(i=1; i <=nlstate; i++){      p2[thetai]=x[thetai]-delti[thetai]/k;
     for(j=1; j <=nlstate+ndeath-1; j++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       fscanf(ficpar,"%1d%1d",&i1,&j1);      k3=func(p2)-fx;
       printf("%1d%1d",i,j);    
       fprintf(ficparo,"%1d%1d",i1,j1);      p2[thetai]=x[thetai]-delti[thetai]/k;
       for(k=1; k<=ncovmodel;k++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         fscanf(ficpar,"%le",&delti3[i][j][k]);      k4=func(p2)-fx;
         printf(" %le",delti3[i][j][k]);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         fprintf(ficparo," %le",delti3[i][j][k]);  #ifdef DEBUG
       }      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       fscanf(ficpar,"\n");      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);
       printf("\n");  #endif
       fprintf(ficparo,"\n");    }
     }    return res;
   }  }
   delti=delti3[1][1];  
    /************** Inverse of matrix **************/
   /* Reads comments: lines beginning with '#' */  void ludcmp(double **a, int n, int *indx, double *d) 
   while((c=getc(ficpar))=='#' && c!= EOF){  { 
     ungetc(c,ficpar);    int i,imax,j,k; 
     fgets(line, MAXLINE, ficpar);    double big,dum,sum,temp; 
     puts(line);    double *vv; 
     fputs(line,ficparo);   
   }    vv=vector(1,n); 
   ungetc(c,ficpar);    *d=1.0; 
      for (i=1;i<=n;i++) { 
   matcov=matrix(1,npar,1,npar);      big=0.0; 
   for(i=1; i <=npar; i++){      for (j=1;j<=n;j++) 
     fscanf(ficpar,"%s",&str);        if ((temp=fabs(a[i][j])) > big) big=temp; 
     printf("%s",str);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     fprintf(ficparo,"%s",str);      vv[i]=1.0/big; 
     for(j=1; j <=i; j++){    } 
       fscanf(ficpar," %le",&matcov[i][j]);    for (j=1;j<=n;j++) { 
       printf(" %.5le",matcov[i][j]);      for (i=1;i<j;i++) { 
       fprintf(ficparo," %.5le",matcov[i][j]);        sum=a[i][j]; 
     }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     fscanf(ficpar,"\n");        a[i][j]=sum; 
     printf("\n");      } 
     fprintf(ficparo,"\n");      big=0.0; 
   }      for (i=j;i<=n;i++) { 
   for(i=1; i <=npar; i++)        sum=a[i][j]; 
     for(j=i+1;j<=npar;j++)        for (k=1;k<j;k++) 
       matcov[i][j]=matcov[j][i];          sum -= a[i][k]*a[k][j]; 
            a[i][j]=sum; 
   printf("\n");        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
           imax=i; 
     /*-------- data file ----------*/        } 
     if((ficres =fopen(fileres,"w"))==NULL) {      } 
       printf("Problem with resultfile: %s\n", fileres);goto end;      if (j != imax) { 
     }        for (k=1;k<=n;k++) { 
     fprintf(ficres,"#%s\n",version);          dum=a[imax][k]; 
              a[imax][k]=a[j][k]; 
     if((fic=fopen(datafile,"r"))==NULL)    {          a[j][k]=dum; 
       printf("Problem with datafile: %s\n", datafile);goto end;        } 
     }        *d = -(*d); 
         vv[imax]=vv[j]; 
     n= lastobs;      } 
     severity = vector(1,maxwav);      indx[j]=imax; 
     outcome=imatrix(1,maxwav+1,1,n);      if (a[j][j] == 0.0) a[j][j]=TINY; 
     num=ivector(1,n);      if (j != n) { 
     moisnais=vector(1,n);        dum=1.0/(a[j][j]); 
     annais=vector(1,n);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     moisdc=vector(1,n);      } 
     andc=vector(1,n);    } 
     agedc=vector(1,n);    free_vector(vv,1,n);  /* Doesn't work */
     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);  void lubksb(double **a, int n, int *indx, double b[]) 
     anint=matrix(1,maxwav,1,n);  { 
     s=imatrix(1,maxwav+1,1,n);    int i,ii=0,ip,j; 
     adl=imatrix(1,maxwav+1,1,n);        double sum; 
     tab=ivector(1,NCOVMAX);   
     ncodemax=ivector(1,8);    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
     i=1;      sum=b[ip]; 
     while (fgets(line, MAXLINE, fic) != NULL)    {      b[ip]=b[i]; 
       if ((i >= firstobs) && (i <=lastobs)) {      if (ii) 
                for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
         for (j=maxwav;j>=1;j--){      else if (sum) ii=i; 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      b[i]=sum; 
           strcpy(line,stra);    } 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    for (i=n;i>=1;i--) { 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      sum=b[i]; 
         }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
              b[i]=sum/a[i][i]; 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    } 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  } 
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  void pstamp(FILE *fichier)
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  {
     fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  }
         for (j=ncov;j>=1;j--){  
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  /************ Frequencies ********************/
         }  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[])
         num[i]=atol(stra);  {  /* Some frequencies */
            
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    int i, m, jk, k1,i1, j1, bool, z1,j;
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/    int first;
     double ***freq; /* Frequencies */
         i=i+1;    double *pp, **prop;
       }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     }    char fileresp[FILENAMELENGTH];
     /* printf("ii=%d", ij);    
        scanf("%d",i);*/    pp=vector(1,nlstate);
   imx=i-1; /* Number of individuals */    prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
   /* for (i=1; i<=imx; i++){    strcat(fileresp,fileres);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    if((ficresp=fopen(fileresp,"w"))==NULL) {
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;      printf("Problem with prevalence resultfile: %s\n", fileresp);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     }      exit(0);
     }
     for (i=1; i<=imx; i++)    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/    j1=0;
     
   /* Calculation of the number of parameter from char model*/    j=cptcoveff;
   Tvar=ivector(1,15);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   Tprod=ivector(1,15);  
   Tvaraff=ivector(1,15);    first=1;
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);          for(k1=1; k1<=j;k1++){
          for(i1=1; i1<=ncodemax[k1];i1++){
   if (strlen(model) >1){        j1++;
     j=0, j1=0, k1=1, k2=1;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     j=nbocc(model,'+');          scanf("%d", i);*/
     j1=nbocc(model,'*');        for (i=-5; i<=nlstate+ndeath; i++)  
     cptcovn=j+1;          for (jk=-5; jk<=nlstate+ndeath; jk++)  
     cptcovprod=j1;            for(m=iagemin; m <= iagemax+3; m++)
                  freq[i][jk][m]=0;
      
     strcpy(modelsav,model);      for (i=1; i<=nlstate; i++)  
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        for(m=iagemin; m <= iagemax+3; m++)
       printf("Error. Non available option model=%s ",model);          prop[i][m]=0;
       goto end;        
     }        dateintsum=0;
            k2cpt=0;
     for(i=(j+1); i>=1;i--){        for (i=1; i<=imx; i++) {
       cutv(stra,strb,modelsav,'+');          bool=1;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);          if  (cptcovn>0) {
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/            for (z1=1; z1<=cptcoveff; z1++) 
       /*scanf("%d",i);*/              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       if (strchr(strb,'*')) {                bool=0;
         cutv(strd,strc,strb,'*');          }
         if (strcmp(strc,"age")==0) {          if (bool==1){
           cptcovprod--;            for(m=firstpass; m<=lastpass; m++){
           cutv(strb,stre,strd,'V');              k2=anint[m][i]+(mint[m][i]/12.);
           Tvar[i]=atoi(stre);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
           cptcovage++;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
             Tage[cptcovage]=i;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
             /*printf("stre=%s ", stre);*/                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
         }                if (m<lastpass) {
         else if (strcmp(strd,"age")==0) {                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           cptcovprod--;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
           cutv(strb,stre,strc,'V');                }
           Tvar[i]=atoi(stre);                
           cptcovage++;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
           Tage[cptcovage]=i;                  dateintsum=dateintsum+k2;
         }                  k2cpt++;
         else {                }
           cutv(strb,stre,strc,'V');                /*}*/
           Tvar[i]=ncov+k1;            }
           cutv(strb,strc,strd,'V');          }
           Tprod[k1]=i;        }
           Tvard[k1][1]=atoi(strc);         
           Tvard[k1][2]=atoi(stre);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
           Tvar[cptcovn+k2]=Tvard[k1][1];        pstamp(ficresp);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        if  (cptcovn>0) {
           for (k=1; k<=lastobs;k++)          fprintf(ficresp, "\n#********** Variable "); 
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           k1++;          fprintf(ficresp, "**********\n#");
           k2=k2+2;        }
         }        for(i=1; i<=nlstate;i++) 
       }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       else {        fprintf(ficresp, "\n");
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        
        /*  scanf("%d",i);*/        for(i=iagemin; i <= iagemax+3; i++){
       cutv(strd,strc,strb,'V');          if(i==iagemax+3){
       Tvar[i]=atoi(strc);            fprintf(ficlog,"Total");
       }          }else{
       strcpy(modelsav,stra);              if(first==1){
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);              first=0;
         scanf("%d",i);*/              printf("See log file for details...\n");
     }            }
 }            fprintf(ficlog,"Age %d", i);
            }
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);          for(jk=1; jk <=nlstate ; jk++){
   printf("cptcovprod=%d ", cptcovprod);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   scanf("%d ",i);*/              pp[jk] += freq[jk][m][i]; 
     fclose(fic);          }
           for(jk=1; jk <=nlstate ; jk++){
     /*  if(mle==1){*/            for(m=-1, pos=0; m <=0 ; m++)
     if (weightopt != 1) { /* Maximisation without weights*/              pos += freq[jk][m][i];
       for(i=1;i<=n;i++) weight[i]=1.0;            if(pp[jk]>=1.e-10){
     }              if(first==1){
     /*-calculation of age at interview from date of interview and age at death -*/                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     agev=matrix(1,maxwav,1,imx);              }
               fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
    for (i=1; i<=imx; i++)            }else{
      for(m=2; (m<= maxwav); m++)              if(first==1)
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
          anint[m][i]=9999;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
          s[m][i]=-1;            }
        }          }
      
     for (i=1; i<=imx; i++)  {          for(jk=1; jk <=nlstate ; jk++){
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       for(m=1; (m<= maxwav); m++){              pp[jk] += freq[jk][m][i];
         if(s[m][i] >0){          }       
           if (s[m][i] == nlstate+1) {          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             if(agedc[i]>0)            pos += pp[jk];
               if(moisdc[i]!=99 && andc[i]!=9999)            posprop += prop[jk][i];
               agev[m][i]=agedc[i];          }
             else {          for(jk=1; jk <=nlstate ; jk++){
               if (andc[i]!=9999){            if(pos>=1.e-5){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);              if(first==1)
               agev[m][i]=-1;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               }              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }            }else{
           }              if(first==1)
           else if(s[m][i] !=9){ /* Should no more exist */                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             if(mint[m][i]==99 || anint[m][i]==9999)            }
               agev[m][i]=1;            if( i <= iagemax){
             else if(agev[m][i] <agemin){              if(pos>=1.e-5){
               agemin=agev[m][i];                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/                /*probs[i][jk][j1]= pp[jk]/pos;*/
             }                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
             else if(agev[m][i] >agemax){              }
               agemax=agev[m][i];              else
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }            }
             /*agev[m][i]=anint[m][i]-annais[i];*/          }
             /*   agev[m][i] = age[i]+2*m;*/          
           }          for(jk=-1; jk <=nlstate+ndeath; jk++)
           else { /* =9 */            for(m=-1; m <=nlstate+ndeath; m++)
             agev[m][i]=1;              if(freq[jk][m][i] !=0 ) {
             s[m][i]=-1;              if(first==1)
           }                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
         }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
         else /*= 0 Unknown */              }
           agev[m][i]=1;          if(i <= iagemax)
       }            fprintf(ficresp,"\n");
              if(first==1)
     }            printf("Others in log...\n");
     for (i=1; i<=imx; i++)  {          fprintf(ficlog,"\n");
       for(m=1; (m<= maxwav); m++){        }
         if (s[m][i] > (nlstate+ndeath)) {      }
           printf("Error: Wrong value in nlstate or ndeath\n");      }
           goto end;    dateintmean=dateintsum/k2cpt; 
         }   
       }    fclose(ficresp);
     }    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
     free_vector(severity,1,maxwav);  }
     free_imatrix(outcome,1,maxwav+1,1,n);  
     free_vector(moisnais,1,n);  /************ Prevalence ********************/
     free_vector(annais,1,n);  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)
     /* free_matrix(mint,1,maxwav,1,n);  {  
        free_matrix(anint,1,maxwav,1,n);*/    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     free_vector(moisdc,1,n);       in each health status at the date of interview (if between dateprev1 and dateprev2).
     free_vector(andc,1,n);       We still use firstpass and lastpass as another selection.
     */
       
     wav=ivector(1,imx);    int i, m, jk, k1, i1, j1, bool, z1,j;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    double ***freq; /* Frequencies */
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    double *pp, **prop;
        double pos,posprop; 
     /* Concatenates waves */    double  y2; /* in fractional years */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    int iagemin, iagemax;
   
     iagemin= (int) agemin;
       Tcode=ivector(1,100);    iagemax= (int) agemax;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    /*pp=vector(1,nlstate);*/
       ncodemax[1]=1;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
          j1=0;
    codtab=imatrix(1,100,1,10);    
    h=0;    j=cptcoveff;
    m=pow(2,cptcoveff);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      
    for(k=1;k<=cptcoveff; k++){    for(k1=1; k1<=j;k1++){
      for(i=1; i <=(m/pow(2,k));i++){      for(i1=1; i1<=ncodemax[k1];i1++){
        for(j=1; j <= ncodemax[k]; j++){        j1++;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        
            h++;        for (i=1; i<=nlstate; i++)  
            if (h>m) h=1;codtab[h][k]=j;          for(m=iagemin; m <= iagemax+3; m++)
          }            prop[i][m]=0.0;
        }       
      }        for (i=1; i<=imx; i++) { /* Each individual */
    }          bool=1;
           if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
    /*for(i=1; i <=m ;i++){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
      for(k=1; k <=cptcovn; k++){                bool=0;
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);          } 
      }          if (bool==1) { 
      printf("\n");            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
    }              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
    scanf("%d",i);*/              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                    if(agev[m][i]==0) agev[m][i]=iagemax+1;
    /* Calculates basic frequencies. Computes observed prevalence at single age                if(agev[m][i]==1) agev[m][i]=iagemax+2;
        and prints on file fileres'p'. */                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); 
                 if (s[m][i]>0 && s[m][i]<=nlstate) { 
                      /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
                      prop[s[m][i]][(int)agev[m][i]] += weight[i];
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                  prop[s[m][i]][iagemax+3] += weight[i]; 
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                } 
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              }
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            } /* end selection of waves */
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          }
              }
     /* For Powell, parameters are in a vector p[] starting at p[1]        for(i=iagemin; i <= iagemax+3; i++){  
        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) */          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
     if(mle==1){          } 
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }          for(jk=1; jk <=nlstate ; jk++){     
                if( i <=  iagemax){ 
     /*--------- results files --------------*/              if(posprop>=1.e-5){ 
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);                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]);
    jk=1;            } 
    fprintf(ficres,"# Parameters\n");          }/* end jk */ 
    printf("# Parameters\n");        }/* end i */ 
    for(i=1,jk=1; i <=nlstate; i++){      } /* end i1 */
      for(k=1; k <=(nlstate+ndeath); k++){    } /* end k1 */
        if (k != i)    
          {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
            printf("%d%d ",i,k);    /*free_vector(pp,1,nlstate);*/
            fprintf(ficres,"%1d%1d ",i,k);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
            for(j=1; j <=ncovmodel; j++){  }  /* End of prevalence */
              printf("%f ",p[jk]);  
              fprintf(ficres,"%f ",p[jk]);  /************* Waves Concatenation ***************/
              jk++;  
            }  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)
            printf("\n");  {
            fprintf(ficres,"\n");    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
          }       Death is a valid wave (if date is known).
      }       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
    }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
  if(mle==1){       and mw[mi+1][i]. dh depends on stepm.
     /* Computing hessian and covariance matrix */       */
     ftolhess=ftol; /* Usually correct */  
     hesscov(matcov, p, npar, delti, ftolhess, func);    int i, mi, m;
  }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     fprintf(ficres,"# Scales\n");       double sum=0., jmean=0.;*/
     printf("# Scales\n");    int first;
      for(i=1,jk=1; i <=nlstate; i++){    int j, k=0,jk, ju, jl;
       for(j=1; j <=nlstate+ndeath; j++){    double sum=0.;
         if (j!=i) {    first=0;
           fprintf(ficres,"%1d%1d",i,j);    jmin=1e+5;
           printf("%1d%1d",i,j);    jmax=-1;
           for(k=1; k<=ncovmodel;k++){    jmean=0.;
             printf(" %.5e",delti[jk]);    for(i=1; i<=imx; i++){
             fprintf(ficres," %.5e",delti[jk]);      mi=0;
             jk++;      m=firstpass;
           }      while(s[m][i] <= nlstate){
           printf("\n");        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
           fprintf(ficres,"\n");          mw[++mi][i]=m;
         }        if(m >=lastpass)
       }          break;
      }        else
              m++;
     k=1;      }/* end while */
     fprintf(ficres,"# Covariance\n");      if (s[m][i] > nlstate){
     printf("# Covariance\n");        mi++;     /* Death is another wave */
     for(i=1;i<=npar;i++){        /* if(mi==0)  never been interviewed correctly before death */
       /*  if (k>nlstate) k=1;           /* Only death is a correct wave */
       i1=(i-1)/(ncovmodel*nlstate)+1;        mw[mi][i]=m;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      }
       printf("%s%d%d",alph[k],i1,tab[i]);*/  
       fprintf(ficres,"%3d",i);      wav[i]=mi;
       printf("%3d",i);      if(mi==0){
       for(j=1; j<=i;j++){        nbwarn++;
         fprintf(ficres," %.5e",matcov[i][j]);        if(first==0){
         printf(" %.5e",matcov[i][j]);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       }          first=1;
       fprintf(ficres,"\n");        }
       printf("\n");        if(first==1){
       k++;          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
     }        }
          } /* end mi==0 */
     while((c=getc(ficpar))=='#' && c!= EOF){    } /* End individuals */
       ungetc(c,ficpar);  
       fgets(line, MAXLINE, ficpar);    for(i=1; i<=imx; i++){
       puts(line);      for(mi=1; mi<wav[i];mi++){
       fputs(line,ficparo);        if (stepm <=0)
     }          dh[mi][i]=1;
     ungetc(c,ficpar);        else{
            if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);            if (agedc[i] < 2*AGESUP) {
                  j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     if (fage <= 2) {              if(j==0) j=1;  /* Survives at least one month after exam */
       bage = agemin;              else if(j<0){
       fage = agemax;                nberr++;
     }                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                    j=1; /* Temporary Dangerous patch */
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                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(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);                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);
                }
     while((c=getc(ficpar))=='#' && c!= EOF){              k=k+1;
     ungetc(c,ficpar);              if (j >= jmax){
     fgets(line, MAXLINE, ficpar);                jmax=j;
     puts(line);                ijmax=i;
     fputs(line,ficparo);              }
   }              if (j <= jmin){
   ungetc(c,ficpar);                jmin=j;
                  ijmin=i;
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);              }
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);              sum=sum+j;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);              /*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);*/
   while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);          else{
     puts(line);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     fputs(line,ficparo);  /*        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]); */
   }  
   ungetc(c,ficpar);            k=k+1;
              if (j >= jmax) {
               jmax=j;
    dateprev1=anprev1+mprev1/12.+jprev1/365.;              ijmax=i;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;            }
             else if (j <= jmin){
   fscanf(ficpar,"pop_based=%d\n",&popbased);              jmin=j;
    fprintf(ficparo,"pop_based=%d\n",popbased);                ijmin=i;
    fprintf(ficres,"pop_based=%d\n",popbased);              }
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   while((c=getc(ficpar))=='#' && c!= EOF){            /*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]);*/
     ungetc(c,ficpar);            if(j<0){
     fgets(line, MAXLINE, ficpar);              nberr++;
     puts(line);              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]);
     fputs(line,ficparo);              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]);
   }            }
   ungetc(c,ficpar);            sum=sum+j;
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);          }
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);          jk= j/stepm;
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);          jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             if(jl==0){
                  dh[mi][i]=jk;
     /*------------ gnuplot -------------*/              bh[mi][i]=0;
     /*chdir(pathcd);*/            }else{ /* We want a negative bias in order to only have interpolation ie
     strcpy(optionfilegnuplot,optionfilefiname);                    * to avoid the price of an extra matrix product in likelihood */
     strcat(optionfilegnuplot,".plt");              dh[mi][i]=jk+1;
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {              bh[mi][i]=ju;
       printf("Problem with file %s",optionfilegnuplot);goto end;            }
     }          }else{
 #ifdef windows            if(jl <= -ju){
     fprintf(ficgp,"cd \"%s\" \n",pathc);              dh[mi][i]=jk;
 #endif              bh[mi][i]=jl;       /* bias is positive if real duration
 m=pow(2,cptcoveff);                                   * is higher than the multiple of stepm and negative otherwise.
                                     */
  /* 1eme*/            }
   for (cpt=1; cpt<= nlstate ; cpt ++) {            else{
    for (k1=1; k1<= m ; k1 ++) {              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
 #ifdef windows            }
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);            if(dh[mi][i]==0){
 #endif              dh[mi][i]=1; /* At least one step */
 #ifdef unix              bh[mi][i]=ju; /* At least one step */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);              /*  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);*/
 #endif            }
           } /* end if mle */
 for (i=1; i<= nlstate ; i ++) {        }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      } /* end wave */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    }
 }    jmean=sum/k;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
     for (i=1; i<= nlstate ; i ++) {    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);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");   }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }  /*********** Tricode ****************************/
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  void tricode(int *Tvar, int **nbcode, int imx)
      for (i=1; i<= nlstate ; i ++) {  {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /* Uses cptcovn+2*cptcovprod as the number of covariates */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /*      Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
 #ifdef unix    int modmaxcovj=0; /* Modality max of covariates j */
 fprintf(ficgp,"\nset ter gif small size 400,300");    cptcoveff=0; 
 #endif   
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    for (k=0; k<maxncov; k++) Ndum[k]=0;
    }    for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
   }  
   /*2 eme*/    for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
       for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the 
   for (k1=1; k1<= m ; k1 ++) {                                 modality of this covariate Vj*/ 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
                                            modality of the nth covariate of individual i. */
     for (i=1; i<= nlstate+1 ; i ++) {        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
       k=2*i;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        if (ij > modmaxcovj) modmaxcovj=ij; 
       for (j=1; j<= nlstate+1 ; j ++) {        /* getting the maximum value of the modality of the covariate
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
   else fprintf(ficgp," \%%*lf (\%%*lf)");           female is 1, then modmaxcovj=1.*/
 }        }
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each modality of model-cov j */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        if( Ndum[i] != 0 )
       for (j=1; j<= nlstate+1 ; j ++) {          ncodemax[j]++; 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        /* Number of modalities of the j th covariate. In fact
         else fprintf(ficgp," \%%*lf (\%%*lf)");           ncodemax[j]=2 (dichotom. variables only) but it could be more for
 }             historical reasons */
       fprintf(ficgp,"\" t\"\" w l 0,");      } /* Ndum[-1] number of undefined modalities */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      ij=1; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
 }          for (k=0; k<= modmaxcovj; k++) { /* k=-1 ? NCOVMAX*//* maxncov or modmaxcovj */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
       else fprintf(ficgp,"\" t\"\" w l 0,");            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
     }                                       k is a modality. If we have model=V1+V1*sex 
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   }            ij++;
            }
   /*3eme*/          if (ij > ncodemax[j]) break; 
         }  /* end of loop on */
   for (k1=1; k1<= m ; k1 ++) {      } /* end of loop on modality */ 
     for (cpt=1; cpt<= nlstate ; cpt ++) {    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
       k=2+nlstate*(cpt-1);    
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);    for (k=0; k< maxncov; k++) Ndum[k]=0;
       for (i=1; i< nlstate ; i ++) {    
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
       }     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
     }     Ndum[ij]++;
   }   }
    
   /* CV preval stat */   ij=1;
   for (k1=1; k1<= m ; k1 ++) {   for (i=1; i<= maxncov; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
     for (cpt=1; cpt<nlstate ; cpt ++) {     if((Ndum[i]!=0) && (i<=ncovcol)){
       k=3;       Tvaraff[ij]=i; /*For printing */
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);       ij++;
       for (i=1; i< nlstate ; i ++)     }
         fprintf(ficgp,"+$%d",k+i+1);   }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);   ij--;
         cptcoveff=ij; /*Number of simple covariates*/
       l=3+(nlstate+ndeath)*cpt;  }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  
       for (i=1; i< nlstate ; i ++) {  /*********** Health Expectancies ****************/
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    {
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    /* Health expectancies, no variances */
     }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   }      int nhstepma, nstepma; /* Decreasing with age */
     double age, agelim, hf;
   /* proba elementaires */    double ***p3mat;
    for(i=1,jk=1; i <=nlstate; i++){    double eip;
     for(k=1; k <=(nlstate+ndeath); k++){  
       if (k != i) {    pstamp(ficreseij);
         for(j=1; j <=ncovmodel; j++){    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/    fprintf(ficreseij,"# Age");
           /*fprintf(ficgp,"%s",alph[1]);*/    for(i=1; i<=nlstate;i++){
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      for(j=1; j<=nlstate;j++){
           jk++;        fprintf(ficreseij," e%1d%1d ",i,j);
           fprintf(ficgp,"\n");      }
         }      fprintf(ficreseij," e%1d. ",i);
       }    }
     }    fprintf(ficreseij,"\n");
     }  
     
   for(jk=1; jk <=m; jk++) {    if(estepm < stepm){
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);      printf ("Problem %d lower than %d\n",estepm, stepm);
    i=1;    }
    for(k2=1; k2<=nlstate; k2++) {    else  hstepm=estepm;   
      k3=i;    /* We compute the life expectancy from trapezoids spaced every estepm months
      for(k=1; k<=(nlstate+ndeath); k++) {     * This is mainly to measure the difference between two models: for example
        if (k != k2){     * if stepm=24 months pijx are given only every 2 years and by summing them
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);     * we are calculating an estimate of the Life Expectancy assuming a linear 
 ij=1;     * progression in between and thus overestimating or underestimating according
         for(j=3; j <=ncovmodel; j++) {     * to the curvature of the survival function. If, for the same date, we 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {     * estimate the model with stepm=1 month, we can keep estepm to 24 months
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);     * to compare the new estimate of Life expectancy with the same linear 
             ij++;     * hypothesis. A more precise result, taking into account a more precise
           }     * curvature will be obtained if estepm is as small as stepm. */
           else  
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /* 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. 
           fprintf(ficgp,")/(1");       nhstepm is the number of hstepm from age to agelim 
               nstepm is the number of stepm from age to agelin. 
         for(k1=1; k1 <=nlstate; k1++){         Look at hpijx to understand the reason of that which relies in memory size
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);       and note for a fixed period like estepm months */
 ij=1;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           for(j=3; j <=ncovmodel; j++){       survival function given by stepm (the optimization length). Unfortunately it
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {       means that if the survival funtion is printed only each two years of age and if
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             ij++;       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 */ 
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
           }    agelim=AGESUP;
           fprintf(ficgp,")");    /* If stepm=6 months */
         }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      
         i=i+ncovmodel;  /* nhstepm age range expressed in number of stepm */
        }    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
      }    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
    }    /* if (stepm >= YEARM) hstepm=1;*/
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   }    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      
   fclose(ficgp);    for (age=bage; age<=fage; age ++){ 
   /* end gnuplot */      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
          /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 chdir(path);      /* if (stepm >= YEARM) hstepm=1;*/
          nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     free_ivector(wav,1,imx);  
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      /* If stepm=6 months */
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        /* Computed by stepm unit matrices, product of hstepma matrices, stored
     free_ivector(num,1,n);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     free_vector(agedc,1,n);      
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     fclose(ficparo);      
     fclose(ficres);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     /*  }*/      
          printf("%d|",(int)age);fflush(stdout);
    /*________fin mle=1_________*/      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
          
       /* Computing expectancies */
        for(i=1; i<=nlstate;i++)
     /* No more information from the sample is required now */        for(j=1; j<=nlstate;j++)
   /* Reads comments: lines beginning with '#' */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   while((c=getc(ficpar))=='#' && c!= EOF){            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     ungetc(c,ficpar);            
     fgets(line, MAXLINE, ficpar);            /* 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]);*/
     puts(line);  
     fputs(line,ficparo);          }
   }  
   ungetc(c,ficpar);      fprintf(ficreseij,"%3.0f",age );
        for(i=1; i<=nlstate;i++){
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);        eip=0;
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);        for(j=1; j<=nlstate;j++){
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          eip +=eij[i][j][(int)age];
 /*--------- index.htm --------*/          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
         }
   strcpy(optionfilehtm,optionfile);        fprintf(ficreseij,"%9.4f", eip );
   strcat(optionfilehtm,".htm");      }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {      fprintf(ficreseij,"\n");
     printf("Problem with %s \n",optionfilehtm);goto end;      
   }    }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">    printf("\n");
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    fprintf(ficlog,"\n");
 Total number of observations=%d <br>    
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>  }
 <hr  size=\"2\" color=\"#EC5E5E\">  
 <li>Outputs files<br><br>\n  void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n  
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>  {
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    /* Covariances of health expectancies eij and of total life expectancies according
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>     to initial status i, ei. .
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    */
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    int nhstepma, nstepma; /* Decreasing with age */
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    double age, agelim, hf;
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>    double ***p3matp, ***p3matm, ***varhe;
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>    double **dnewm,**doldm;
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    double *xp, *xm;
     double **gp, **gm;
  fprintf(fichtm," <li>Graphs</li><p>");    double ***gradg, ***trgradg;
     int theta;
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    double eip, vip;
   
  j1=0;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
  for(k1=1; k1<=m;k1++){    xp=vector(1,npar);
    for(i1=1; i1<=ncodemax[k1];i1++){    xm=vector(1,npar);
        j1++;    dnewm=matrix(1,nlstate*nlstate,1,npar);
        if (cptcovn > 0) {    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    
          for (cpt=1; cpt<=cptcoveff;cpt++)    pstamp(ficresstdeij);
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    fprintf(ficresstdeij,"# Age");
        }    for(i=1; i<=nlstate;i++){
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      for(j=1; j<=nlstate;j++)
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
        for(cpt=1; cpt<nlstate;cpt++){      fprintf(ficresstdeij," e%1d. ",i);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    }
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    fprintf(ficresstdeij,"\n");
        }  
     for(cpt=1; cpt<=nlstate;cpt++) {    pstamp(ficrescveij);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
 interval) in state (%d): v%s%d%d.gif <br>    fprintf(ficrescveij,"# Age");
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      for(i=1; i<=nlstate;i++)
      }      for(j=1; j<=nlstate;j++){
      for(cpt=1; cpt<=nlstate;cpt++) {        cptj= (j-1)*nlstate+i;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        for(i2=1; i2<=nlstate;i2++)
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          for(j2=1; j2<=nlstate;j2++){
      }            cptj2= (j2-1)*nlstate+i2;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            if(cptj2 <= cptj)
 health expectancies in states (1) and (2): e%s%d.gif<br>              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          }
 fprintf(fichtm,"\n</body>");      }
    }    fprintf(ficrescveij,"\n");
  }    
 fclose(fichtm);    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   /*--------------- Prevalence limit --------------*/    }
      else  hstepm=estepm;   
   strcpy(filerespl,"pl");    /* We compute the life expectancy from trapezoids spaced every estepm months
   strcat(filerespl,fileres);     * This is mainly to measure the difference between two models: for example
   if((ficrespl=fopen(filerespl,"w"))==NULL) {     * if stepm=24 months pijx are given only every 2 years and by summing them
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;     * we are calculating an estimate of the Life Expectancy assuming a linear 
   }     * progression in between and thus overestimating or underestimating according
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);     * to the curvature of the survival function. If, for the same date, we 
   fprintf(ficrespl,"#Prevalence limit\n");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   fprintf(ficrespl,"#Age ");     * to compare the new estimate of Life expectancy with the same linear 
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);     * hypothesis. A more precise result, taking into account a more precise
   fprintf(ficrespl,"\n");     * curvature will be obtained if estepm is as small as stepm. */
    
   prlim=matrix(1,nlstate,1,nlstate);    /* For example we decided to compute the life expectancy with the smallest unit */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       nhstepm is the number of hstepm from age to agelim 
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       nstepm is the number of stepm from age to agelin. 
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       Look at hpijx to understand the reason of that which relies in memory size
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */       and note for a fixed period like estepm months */
   k=0;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   agebase=agemin;       survival function given by stepm (the optimization length). Unfortunately it
   agelim=agemax;       means that if the survival funtion is printed only each two years of age and if
   ftolpl=1.e-10;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   i1=cptcoveff;       results. So we changed our mind and took the option of the best precision.
   if (cptcovn < 1){i1=1;}    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    /* If stepm=6 months */
         k=k+1;    /* nhstepm age range expressed in number of stepm */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    agelim=AGESUP;
         fprintf(ficrespl,"\n#******");    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
         for(j=1;j<=cptcoveff;j++)    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* if (stepm >= YEARM) hstepm=1;*/
         fprintf(ficrespl,"******\n");    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
            
         for (age=agebase; age<=agelim; age++){    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespl,"%.0f",age );    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
           for(i=1; i<=nlstate;i++)    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
           fprintf(ficrespl," %.5f", prlim[i][i]);    gp=matrix(0,nhstepm,1,nlstate*nlstate);
           fprintf(ficrespl,"\n");    gm=matrix(0,nhstepm,1,nlstate*nlstate);
         }  
       }    for (age=bage; age<=fage; age ++){ 
     }      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
   fclose(ficrespl);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
   /*------------- h Pij x at various ages ------------*/      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      /* If stepm=6 months */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      /* Computed by stepm unit matrices, product of hstepma matrices, stored
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   }      
   printf("Computing pij: result on file '%s' \n", filerespij);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    
   stepsize=(int) (stepm+YEARM-1)/YEARM;      /* Computing  Variances of health expectancies */
   /*if (stepm<=24) stepsize=2;*/      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
   agelim=AGESUP;      for(theta=1; theta <=npar; theta++){
   hstepm=stepsize*YEARM; /* Every year of age */        for(i=1; i<=npar; i++){ 
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
            xm[i] = x[i] - (i==theta ?delti[theta]:0);
   k=0;        }
   for(cptcov=1;cptcov<=i1;cptcov++){        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
       k=k+1;    
         fprintf(ficrespij,"\n#****** ");        for(j=1; j<= nlstate; j++){
         for(j=1;j<=cptcoveff;j++)          for(i=1; i<=nlstate; i++){
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for(h=0; h<=nhstepm-1; h++){
         fprintf(ficrespij,"******\n");              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
                      gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
         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 */        }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       
           oldm=oldms;savm=savms;        for(ij=1; ij<= nlstate*nlstate; ij++)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for(h=0; h<=nhstepm-1; h++){
           fprintf(ficrespij,"# Age");            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           for(i=1; i<=nlstate;i++)          }
             for(j=1; j<=nlstate+ndeath;j++)      }/* End theta */
               fprintf(ficrespij," %1d-%1d",i,j);      
           fprintf(ficrespij,"\n");      
           for (h=0; h<=nhstepm; h++){      for(h=0; h<=nhstepm-1; h++)
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        for(j=1; j<=nlstate*nlstate;j++)
             for(i=1; i<=nlstate;i++)          for(theta=1; theta <=npar; theta++)
               for(j=1; j<=nlstate+ndeath;j++)            trgradg[h][j][theta]=gradg[h][theta][j];
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      
             fprintf(ficrespij,"\n");  
           }       for(ij=1;ij<=nlstate*nlstate;ij++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(ji=1;ji<=nlstate*nlstate;ji++)
           fprintf(ficrespij,"\n");          varhe[ij][ji][(int)age] =0.;
         }  
     }       printf("%d|",(int)age);fflush(stdout);
   }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/        for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   fclose(ficrespij);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(ij=1;ij<=nlstate*nlstate;ij++)
   if(stepm == 1) {            for(ji=1;ji<=nlstate*nlstate;ji++)
   /*---------- Forecasting ------------------*/              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;        }
       }
   /*printf("calage= %f", calagedate);*/  
        /* Computing expectancies */
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
   strcpy(fileresf,"f");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   strcat(fileresf,fileres);            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
   if((ficresf=fopen(fileresf,"w"))==NULL) {            
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   }  
   printf("Computing forecasting: result on file '%s' \n", fileresf);          }
   
   free_matrix(mint,1,maxwav,1,n);      fprintf(ficresstdeij,"%3.0f",age );
   free_matrix(anint,1,maxwav,1,n);      for(i=1; i<=nlstate;i++){
   free_matrix(agev,1,maxwav,1,imx);        eip=0.;
   /* Mobile average */        vip=0.;
         for(j=1; j<=nlstate;j++){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
   if (mobilav==1) {            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)        }
       for (i=1; i<=nlstate;i++)        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      }
           mobaverage[(int)agedeb][i][cptcod]=0.;      fprintf(ficresstdeij,"\n");
      
     for (agedeb=bage+4; agedeb<=fage; agedeb++){      fprintf(ficrescveij,"%3.0f",age );
       for (i=1; i<=nlstate;i++){      for(i=1; i<=nlstate;i++)
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for(j=1; j<=nlstate;j++){
           for (cpt=0;cpt<=4;cpt++){          cptj= (j-1)*nlstate+i;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          for(i2=1; i2<=nlstate;i2++)
           }            for(j2=1; j2<=nlstate;j2++){
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;              cptj2= (j2-1)*nlstate+i2;
         }              if(cptj2 <= cptj)
       }                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
     }              }
   }        }
       fprintf(ficrescveij,"\n");
   stepsize=(int) (stepm+YEARM-1)/YEARM;     
   if (stepm<=12) stepsize=1;    }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   agelim=AGESUP;    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   /*hstepm=stepsize*YEARM; *//* Every year of age */    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   hstepm=1;    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   yp1=modf(dateintmean,&yp);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   anprojmean=yp;    printf("\n");
   yp2=modf((yp1*12),&yp);    fprintf(ficlog,"\n");
   mprojmean=yp;  
   yp1=modf((yp2*30.5),&yp);    free_vector(xm,1,npar);
   jprojmean=yp;    free_vector(xp,1,npar);
   if(jprojmean==0) jprojmean=1;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   if(mprojmean==0) jprojmean=1;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);  }
   
   if (popforecast==1) {  /************ Variance ******************/
     if((ficpop=fopen(popfile,"r"))==NULL)    {  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
       printf("Problem with population file : %s\n",popfile);goto end;  {
     }    /* Variance of health expectancies */
     popage=ivector(0,AGESUP);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     popeffectif=vector(0,AGESUP);    /* double **newm;*/
     popcount=vector(0,AGESUP);    double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     i=1;      int i, j, nhstepm, hstepm, h, nstepm ;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)    int k, cptcode;
       {    double *xp;
         i=i+1;    double **gp, **gm;  /* for var eij */
       }    double ***gradg, ***trgradg; /*for var eij */
     imx=i;    double **gradgp, **trgradgp; /* for var p point j */
        double *gpp, *gmp; /* for var p point j */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   }    double ***p3mat;
     double age,agelim, hf;
   for(cptcov=1;cptcov<=i1;cptcov++){    double ***mobaverage;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    int theta;
       k=k+1;    char digit[4];
       fprintf(ficresf,"\n#******");    char digitp[25];
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    char fileresprobmorprev[FILENAMELENGTH];
       }  
       fprintf(ficresf,"******\n");    if(popbased==1){
       fprintf(ficresf,"# StartingAge FinalAge");      if(mobilav!=0)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        strcpy(digitp,"-populbased-mobilav-");
       if (popforecast==1)  fprintf(ficresf," [Population]");      else strcpy(digitp,"-populbased-nomobil-");
        }
       for (cpt=0; cpt<4;cpt++) {    else 
         fprintf(ficresf,"\n");      strcpy(digitp,"-stablbased-");
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
     if (mobilav!=0) {
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         nhstepm = nhstepm/hstepm;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
         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);      strcpy(fileresprobmorprev,"prmorprev"); 
            sprintf(digit,"%-d",ij);
         for (h=0; h<=nhstepm; h++){    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
           if (h==(int) (calagedate+YEARM*cpt)) {    strcat(fileresprobmorprev,digit); /* Tvar to be done */
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
           }    strcat(fileresprobmorprev,fileres);
           for(j=1; j<=nlstate+ndeath;j++) {    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
             kk1=0.;kk2=0;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
             for(i=1; i<=nlstate;i++) {              fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
               if (mobilav==1)    }
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
               else {   
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/    pstamp(ficresprobmorprev);
               }    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
             }      fprintf(ficresprobmorprev," p.%-d SE",j);
                for(i=1; i<=nlstate;i++)
             if (h==(int)(calagedate+12*cpt)){        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
               fprintf(ficresf," %.3f", kk1);    }  
                  fprintf(ficresprobmorprev,"\n");
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);    fprintf(ficgp,"\n# Routine varevsij");
             }    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
           }    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
         }    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*   } */
       }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       }    pstamp(ficresvij);
     }    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
   }    if(popbased==1)
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      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);
   if (popforecast==1) {    else
     free_ivector(popage,0,AGESUP);      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     free_vector(popeffectif,0,AGESUP);    fprintf(ficresvij,"# Age");
     free_vector(popcount,0,AGESUP);    for(i=1; i<=nlstate;i++)
   }      for(j=1; j<=nlstate;j++)
   free_imatrix(s,1,maxwav+1,1,n);        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
   free_vector(weight,1,n);    fprintf(ficresvij,"\n");
   fclose(ficresf);  
   }/* End forecasting */    xp=vector(1,npar);
   else{    dnewm=matrix(1,nlstate,1,npar);
     erreur=108;    doldm=matrix(1,nlstate,1,nlstate);
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
   /*---------- Health expectancies and variances ------------*/    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
   strcpy(filerest,"t");    gmp=vector(nlstate+1,nlstate+ndeath);
   strcat(filerest,fileres);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   if((ficrest=fopen(filerest,"w"))==NULL) {    
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
   strcpy(filerese,"e");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   strcat(filerese,fileres);       nhstepm is the number of hstepm from age to agelim 
   if((ficreseij=fopen(filerese,"w"))==NULL) {       nstepm is the number of stepm from age to agelin. 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);       Look at function hpijx to understand why (it is linked to memory size questions) */
   }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
  strcpy(fileresv,"v");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   strcat(fileresv,fileres);       results. So we changed our mind and took the option of the best precision.
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   }    agelim = AGESUP;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   k=0;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   for(cptcov=1;cptcov<=i1;cptcov++){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       k=k+1;      gp=matrix(0,nhstepm,1,nlstate);
       fprintf(ficrest,"\n#****** ");      gm=matrix(0,nhstepm,1,nlstate);
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficrest,"******\n");      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       fprintf(ficreseij,"\n#****** ");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       for(j=1;j<=cptcoveff;j++)        }
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       fprintf(ficreseij,"******\n");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
       fprintf(ficresvij,"\n#****** ");        if (popbased==1) {
       for(j=1;j<=cptcoveff;j++)          if(mobilav ==0){
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);            for(i=1; i<=nlstate;i++)
       fprintf(ficresvij,"******\n");              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);            for(i=1; i<=nlstate;i++)
       oldm=oldms;savm=savms;              prlim[i][i]=mobaverage[(int)age][i][ij];
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);            }
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        }
       oldm=oldms;savm=savms;    
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        for(j=1; j<= nlstate; j++){
                for(h=0; h<=nhstepm; h++){
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
       fprintf(ficrest,"\n");          }
                }
       hf=1;        /* This for computing probability of death (h=1 means
       if (stepm >= YEARM) hf=stepm/YEARM;           computed over hstepm matrices product = hstepm*stepm months) 
       epj=vector(1,nlstate+1);           as a weighted average of prlim.
       for(age=bage; age <=fage ;age++){        */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         if (popbased==1) {          for(i=1,gpp[j]=0.; i<= nlstate; i++)
           for(i=1; i<=nlstate;i++)            gpp[j] += prlim[i][i]*p3mat[i][j][1];
             prlim[i][i]=probs[(int)age][i][k];        }    
         }        /* end probability of death */
          
         fprintf(ficrest," %.0f",age);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           }   
           epj[nlstate+1] +=epj[j];        if (popbased==1) {
         }          if(mobilav ==0){
         for(i=1, vepp=0.;i <=nlstate;i++)            for(i=1; i<=nlstate;i++)
           for(j=1;j <=nlstate;j++)              prlim[i][i]=probs[(int)age][i][ij];
             vepp += vareij[i][j][(int)age];          }else{ /* mobilav */ 
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));            for(i=1; i<=nlstate;i++)
         for(j=1;j <=nlstate;j++){              prlim[i][i]=mobaverage[(int)age][i][ij];
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));          }
         }        }
         fprintf(ficrest,"\n");  
       }        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
     }          for(h=0; h<=nhstepm; h++){
   }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                      gm[h][j] += prlim[i][i]*p3mat[i][j][h];
                  }
         }
         /* This for computing probability of death (h=1 means
  fclose(ficreseij);           computed over hstepm matrices product = hstepm*stepm months) 
  fclose(ficresvij);           as a weighted average of prlim.
   fclose(ficrest);        */
   fclose(ficpar);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   free_vector(epj,1,nlstate+1);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   /*  scanf("%d ",i); */           gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
   /*------- Variance limit prevalence------*/          /* end probability of death */
   
 strcpy(fileresvpl,"vpl");        for(j=1; j<= nlstate; j++) /* vareij */
   strcat(fileresvpl,fileres);          for(h=0; h<=nhstepm; h++){
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);          }
     exit(0);  
   }        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
  k=0;  
  for(cptcov=1;cptcov<=i1;cptcov++){      } /* End theta */
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
      k=k+1;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
      fprintf(ficresvpl,"\n#****** ");  
      for(j=1;j<=cptcoveff;j++)      for(h=0; h<=nhstepm; h++) /* veij */
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=1; j<=nlstate;j++)
      fprintf(ficresvpl,"******\n");          for(theta=1; theta <=npar; theta++)
                  trgradg[h][j][theta]=gradg[h][theta][j];
      varpl=matrix(1,nlstate,(int) bage, (int) fage);  
      oldm=oldms;savm=savms;      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        for(theta=1; theta <=npar; theta++)
    }          trgradgp[j][theta]=gradgp[theta][j];
  }    
   
   fclose(ficresvpl);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
   /*---------- End : free ----------------*/        for(j=1;j<=nlstate;j++)
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          vareij[i][j][(int)age] =0.;
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      for(h=0;h<=nhstepm;h++){
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        for(k=0;k<=nhstepm;k++){
            matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          for(i=1;i<=nlstate;i++)
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);            for(j=1;j<=nlstate;j++)
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        }
        }
   free_matrix(matcov,1,npar,1,npar);    
   free_vector(delti,1,npar);      /* pptj */
        matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
   if(erreur >0)        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     printf("End of Imach with error %d\n",erreur);          varppt[j][i]=doldmp[j][i];
   else   printf("End of Imach\n");      /* end ppptj */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      /*  x centered again */
        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   /* 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);*/      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   /*printf("Total time was %d uSec.\n", total_usecs);*/   
   /*------ End -----------*/      if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
  end:            prlim[i][i]=probs[(int)age][i][ij];
 #ifdef windows        }else{ /* mobilav */ 
   /* chdir(pathcd);*/          for(i=1; i<=nlstate;i++)
 #endif            prlim[i][i]=mobaverage[(int)age][i][ij];
  /*system("wgnuplot graph.plt");*/        }
  /*system("../gp37mgw/wgnuplot graph.plt");*/      }
  /*system("cd ../gp37mgw");*/               
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      /* This for computing probability of death (h=1 means
  strcpy(plotcmd,GNUPLOTPROGRAM);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
  strcat(plotcmd," ");         as a weighted average of prlim.
  strcat(plotcmd,optionfilegnuplot);      */
  system(plotcmd);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
 #ifdef windows          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   while (z[0] != 'q') {      }    
     chdir(path);      /* end probability of death */
     printf("\nType e to edit output files, c to start again, and q for exiting: ");  
     scanf("%s",z);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     if (z[0] == 'c') system("./imach");      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     else if (z[0] == 'e') {        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       chdir(path);        for(i=1; i<=nlstate;i++){
       system(optionfilehtm);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     }        }
     else if (z[0] == 'q') exit(0);      } 
   }      fprintf(ficresprobmorprev,"\n");
 #endif  
 }      fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       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);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   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));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     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);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     int k, cptcode;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           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];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
     xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   and drawn. It helps understanding how is the covariance between two incidences.\
    They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
   It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       printf("Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);
                       lc1=fabs(lc1);
                       lc2=fabs(lc2);
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   
   int decodemodel ( char model[], int lastobs)
   {
     int i, j, k;
     int i1, j1, k1, k2;
     char modelsav[80];
      char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3 
                     but the covariates which are product must be computed and stored. */
       cptcovprod=j1; /*Number of products  V1*V2 +v3*age = 2 */
       
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       for(k=cptcovn; k>=1;k--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 
                                       */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn: strb=V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V'); /* stre="V3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=2 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1;  /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1]=atoi(strc); /* m 1 for V1*/
             Tvard[k1][2]=atoi(stre); /* n 4 for V4*/
             Tvar[cptcovn+k2]=Tvard[k1][1]; /* Tvar[(cptcovn=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovn+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovn=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
             k1++;
             k2=k2+2;
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutv(strd,strc,strb,'V');
           Tvar[k]=atoi(strc);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       cptcovn=nbocc(model,'+')+1;
     /* ncovprod */
     ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8); /* hard coded ? */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,15); 
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2); /* For V3*V2 Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,15); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) {
               h=1;
               codtab[h][k]=j;
               codtab[h][Tvar[k]]=j;
             }
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #elsedef
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #elsedef
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /* to clean */
           printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         }
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms;
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);   fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
    endfree:
     free_matrix(prlim,1,nlstate,1,nlstate);
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   
Removed from v.1.22  
changed lines
  Added in v.1.138

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