Diff for /imach/src/imach.c between versions 1.30 and 1.145

version 1.30, 2002/03/08 16:17:18 version 1.145, 2014/06/10 21:23:15
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.145  2014/06/10 21:23:15  brouard
      Summary: Debugging with valgrind
   This program computes Healthy Life Expectancies from    Author: Nicolas Brouard
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  
   first survey ("cross") where individuals from different ages are    Lot of changes in order to output the results with some covariates
   interviewed on their health status or degree of disability (in the    After the Edimburgh REVES conference 2014, it seems mandatory to
   case of a health survey which is our main interest) -2- at least a    improve the code.
   second wave of interviews ("longitudinal") which measure each change    No more memory valgrind error but a lot has to be done in order to
   (if any) in individual health status.  Health expectancies are    continue the work of splitting the code into subroutines.
   computed from the time spent in each health state according to a    Also, decodemodel has been improved. Tricode is still not
   model. More health states you consider, more time is necessary to reach the    optimal. nbcode should be improved. Documentation has been added in
   Maximum Likelihood of the parameters involved in the model.  The    the source code.
   simplest model is the multinomial logistic model where pij is the  
   probabibility to be observed in state j at the second wave    Revision 1.143  2014/01/26 09:45:38  brouard
   conditional to be observed in state i at the first wave. Therefore    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   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    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   complex model than "constant and age", you should modify the program    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   where the markup *Covariates have to be included here again* invites  
   you to do it.  More covariates you add, slower the    Revision 1.142  2014/01/26 03:57:36  brouard
   convergence.    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   
   The advantage of this computer programme, compared to a simple    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.141  2014/01/26 02:42:01  brouard
   intermediate interview, the information is lost, but taken into    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   account using an interpolation or extrapolation.    
     Revision 1.140  2011/09/02 10:37:54  brouard
   hPijx is the probability to be observed in state i at age x+h    Summary: times.h is ok with mingw32 now.
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.139  2010/06/14 07:50:17  brouard
   states. This elementary transition (by month or quarter trimester,    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
   semester or year) is model as a multinomial logistic.  The hPx    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.138  2010/04/30 18:19:40  brouard
   hPijx.    *** empty log message ***
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.137  2010/04/29 18:11:38  brouard
   of the life expectancies. It also computes the prevalence limits.    (Module): Checking covariates for more complex models
      than V1+V2. A lot of change to be done. Unstable.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.136  2010/04/26 20:30:53  brouard
   This software have been partly granted by Euro-REVES, a concerted action    (Module): merging some libgsl code. Fixing computation
   from the European Union.    of likelione (using inter/intrapolation if mle = 0) in order to
   It is copyrighted identically to a GNU software product, ie programme and    get same likelihood as if mle=1.
   software can be distributed freely for non commercial use. Latest version    Some cleaning of code and comments added.
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.135  2009/10/29 15:33:14  brouard
      (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #include <math.h>  
 #include <stdio.h>    Revision 1.134  2009/10/29 13:18:53  brouard
 #include <stdlib.h>    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #include <unistd.h>  
     Revision 1.133  2009/07/06 10:21:25  brouard
 #define MAXLINE 256    just nforces
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"  
 #define FILENAMELENGTH 80    Revision 1.132  2009/07/06 08:22:05  brouard
 /*#define DEBUG*/    Many tings
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.131  2009/06/20 16:22:47  brouard
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Some dimensions resccaled
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.130  2009/05/26 06:44:34  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (Module): Max Covariate is now set to 20 instead of 8. A
     lot of cleaning with variables initialized to 0. Trying to make
 #define NINTERVMAX 8    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.129  2007/08/31 13:49:27  lievre
 #define NCOVMAX 8 /* Maximum number of covariates */    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.128  2006/06/30 13:02:05  brouard
 #define AGESUP 130    (Module): Clarifications on computing e.j
 #define AGEBASE 40  
     Revision 1.127  2006/04/28 18:11:50  brouard
     (Module): Yes the sum of survivors was wrong since
 int erreur; /* Error number */    imach-114 because nhstepm was no more computed in the age
 int nvar;    loop. Now we define nhstepma in the age loop.
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    (Module): In order to speed up (in case of numerous covariates) we
 int npar=NPARMAX;    compute health expectancies (without variances) in a first step
 int nlstate=2; /* Number of live states */    and then all the health expectancies with variances or standard
 int ndeath=1; /* Number of dead states */    deviation (needs data from the Hessian matrices) which slows the
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    computation.
 int popbased=0;    In the future we should be able to stop the program is only health
     expectancies and graph are needed without standard deviations.
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.126  2006/04/28 17:23:28  brouard
 int jmin, jmax; /* min, max spacing between 2 waves */    (Module): Yes the sum of survivors was wrong since
 int mle, weightopt;    imach-114 because nhstepm was no more computed in the age
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    loop. Now we define nhstepma in the age loop.
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Version 0.98h
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.125  2006/04/04 15:20:31  lievre
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Errors in calculation of health expectancies. Age was not initialized.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Forecasting file added.
 FILE *ficgp,*ficresprob,*ficpop;  
 FILE *ficreseij;    Revision 1.124  2006/03/22 17:13:53  lievre
   char filerese[FILENAMELENGTH];    Parameters are printed with %lf instead of %f (more numbers after the comma).
  FILE  *ficresvij;    The log-likelihood is printed in the log file
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.123  2006/03/20 10:52:43  brouard
   char fileresvpl[FILENAMELENGTH];    * imach.c (Module): <title> changed, corresponds to .htm file
     name. <head> headers where missing.
 #define NR_END 1  
 #define FREE_ARG char*    * imach.c (Module): Weights can have a decimal point as for
 #define FTOL 1.0e-10    English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
 #define NRANSI    Modification of warning when the covariates values are not 0 or
 #define ITMAX 200    1.
     Version 0.98g
 #define TOL 2.0e-4  
     Revision 1.122  2006/03/20 09:45:41  brouard
 #define CGOLD 0.3819660    (Module): Weights can have a decimal point as for
 #define ZEPS 1.0e-10    English (a comma might work with a correct LC_NUMERIC environment,
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 #define GOLD 1.618034    1.
 #define GLIMIT 100.0    Version 0.98g
 #define TINY 1.0e-20  
     Revision 1.121  2006/03/16 17:45:01  lievre
 static double maxarg1,maxarg2;    * imach.c (Module): Comments concerning covariates added
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    * imach.c (Module): refinements in the computation of lli if
      status=-2 in order to have more reliable computation if stepm is
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    not 1 month. Version 0.98f
 #define rint(a) floor(a+0.5)  
     Revision 1.120  2006/03/16 15:10:38  lievre
 static double sqrarg;    (Module): refinements in the computation of lli if
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    status=-2 in order to have more reliable computation if stepm is
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    not 1 month. Version 0.98f
   
 int imx;    Revision 1.119  2006/03/15 17:42:26  brouard
 int stepm;    (Module): Bug if status = -2, the loglikelihood was
 /* Stepm, step in month: minimum step interpolation*/    computed as likelihood omitting the logarithm. Version O.98e
   
 int m,nb;    Revision 1.118  2006/03/14 18:20:07  brouard
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    (Module): varevsij Comments added explaining the second
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    table of variances if popbased=1 .
 double **pmmij, ***probs, ***mobaverage;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 double dateintmean=0;    (Module): Function pstamp added
     (Module): Version 0.98d
 double *weight;  
 int **s; /* Status */    Revision 1.117  2006/03/14 17:16:22  brouard
 double *agedc, **covar, idx;    (Module): varevsij Comments added explaining the second
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    table of variances if popbased=1 .
     (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    (Module): Function pstamp added
 double ftolhess; /* Tolerance for computing hessian */    (Module): Version 0.98d
   
 /**************** split *************************/    Revision 1.116  2006/03/06 10:29:27  brouard
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    (Module): Variance-covariance wrong links and
 {    varian-covariance of ej. is needed (Saito).
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */    Revision 1.115  2006/02/27 12:17:45  brouard
     (Module): One freematrix added in mlikeli! 0.98c
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.114  2006/02/26 12:57:58  brouard
 #ifdef windows    (Module): Some improvements in processing parameter
    s = strrchr( path, '\\' );           /* find last / */    filename with strsep.
 #else  
    s = strrchr( path, '/' );            /* find last / */    Revision 1.113  2006/02/24 14:20:24  brouard
 #endif    (Module): Memory leaks checks with valgrind and:
    if ( s == NULL ) {                   /* no directory, so use current */    datafile was not closed, some imatrix were not freed and on matrix
 #if     defined(__bsd__)                /* get current working directory */    allocation too.
       extern char       *getwd( );  
     Revision 1.112  2006/01/30 09:55:26  brouard
       if ( getwd( dirc ) == NULL ) {    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 #else  
       extern char       *getcwd( );    Revision 1.111  2006/01/25 20:38:18  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    (Module): Comments can be added in data file. Missing date values
 #endif    can be a simple dot '.'.
          return( GLOCK_ERROR_GETCWD );  
       }    Revision 1.110  2006/01/25 00:51:50  brouard
       strcpy( name, path );             /* we've got it */    (Module): Lots of cleaning and bugs added (Gompertz)
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Revision 1.109  2006/01/24 19:37:15  brouard
       l2 = strlen( s );                 /* length of filename */    (Module): Comments (lines starting with a #) are allowed in data.
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Revision 1.108  2006/01/19 18:05:42  lievre
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Gnuplot problem appeared...
       dirc[l1-l2] = 0;                  /* add zero */    To be fixed
    }  
    l1 = strlen( dirc );                 /* length of directory */    Revision 1.107  2006/01/19 16:20:37  brouard
 #ifdef windows    Test existence of gnuplot in imach path
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else    Revision 1.106  2006/01/19 13:24:36  brouard
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    Some cleaning and links added in html output
 #endif  
    s = strrchr( name, '.' );            /* find last / */    Revision 1.105  2006/01/05 20:23:19  lievre
    s++;    *** empty log message ***
    strcpy(ext,s);                       /* save extension */  
    l1= strlen( name);    Revision 1.104  2005/09/30 16:11:43  lievre
    l2= strlen( s)+1;    (Module): sump fixed, loop imx fixed, and simplifications.
    strncpy( finame, name, l1-l2);    (Module): If the status is missing at the last wave but we know
    finame[l1-l2]= 0;    that the person is alive, then we can code his/her status as -2
    return( 0 );                         /* we're done */    (instead of missing=-1 in earlier versions) and his/her
 }    contributions to the likelihood is 1 - Prob of dying from last
     health status (= 1-p13= p11+p12 in the easiest case of somebody in
     the healthy state at last known wave). Version is 0.98
 /******************************************/  
     Revision 1.103  2005/09/30 15:54:49  lievre
 void replace(char *s, char*t)    (Module): sump fixed, loop imx fixed, and simplifications.
 {  
   int i;    Revision 1.102  2004/09/15 17:31:30  brouard
   int lg=20;    Add the possibility to read data file including tab characters.
   i=0;  
   lg=strlen(t);    Revision 1.101  2004/09/15 10:38:38  brouard
   for(i=0; i<= lg; i++) {    Fix on curr_time
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    Revision 1.100  2004/07/12 18:29:06  brouard
   }    Add version for Mac OS X. Just define UNIX in Makefile
 }  
     Revision 1.99  2004/06/05 08:57:40  brouard
 int nbocc(char *s, char occ)    *** empty log message ***
 {  
   int i,j=0;    Revision 1.98  2004/05/16 15:05:56  brouard
   int lg=20;    New version 0.97 . First attempt to estimate force of mortality
   i=0;    directly from the data i.e. without the need of knowing the health
   lg=strlen(s);    state at each age, but using a Gompertz model: log u =a + b*age .
   for(i=0; i<= lg; i++) {    This is the basic analysis of mortality and should be done before any
   if  (s[i] == occ ) j++;    other analysis, in order to test if the mortality estimated from the
   }    cross-longitudinal survey is different from the mortality estimated
   return j;    from other sources like vital statistic data.
 }  
     The same imach parameter file can be used but the option for mle should be -3.
 void cutv(char *u,char *v, char*t, char occ)  
 {    Agnès, who wrote this part of the code, tried to keep most of the
   int i,lg,j,p=0;    former routines in order to include the new code within the former code.
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    The output is very simple: only an estimate of the intercept and of
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    the slope with 95% confident intervals.
   }  
     Current limitations:
   lg=strlen(t);    A) Even if you enter covariates, i.e. with the
   for(j=0; j<p; j++) {    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
     (u[j] = t[j]);    B) There is no computation of Life Expectancy nor Life Table.
   }  
      u[p]='\0';    Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
    for(j=0; j<= lg; j++) {    suppressed.
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }    Revision 1.96  2003/07/15 15:38:55  brouard
 }    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     rewritten within the same printf. Workaround: many printfs.
 /********************** nrerror ********************/  
     Revision 1.95  2003/07/08 07:54:34  brouard
 void nrerror(char error_text[])    * imach.c (Repository):
 {    (Repository): Using imachwizard code to output a more meaningful covariance
   fprintf(stderr,"ERREUR ...\n");    matrix (cov(a12,c31) instead of numbers.
   fprintf(stderr,"%s\n",error_text);  
   exit(1);    Revision 1.94  2003/06/27 13:00:02  brouard
 }    Just cleaning
 /*********************** vector *******************/  
 double *vector(int nl, int nh)    Revision 1.93  2003/06/25 16:33:55  brouard
 {    (Module): On windows (cygwin) function asctime_r doesn't
   double *v;    exist so I changed back to asctime which exists.
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    (Module): Version 0.96b
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    Revision 1.92  2003/06/25 16:30:45  brouard
 }    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    Revision 1.91  2003/06/25 15:30:29  brouard
 {    * imach.c (Repository): Duplicated warning errors corrected.
   free((FREE_ARG)(v+nl-NR_END));    (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
 /************************ivector *******************************/    concerning matrix of covariance. It has extension -cov.htm.
 int *ivector(long nl,long nh)  
 {    Revision 1.90  2003/06/24 12:34:15  brouard
   int *v;    (Module): Some bugs corrected for windows. Also, when
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    mle=-1 a template is output in file "or"mypar.txt with the design
   if (!v) nrerror("allocation failure in ivector");    of the covariance matrix to be input.
   return v-nl+NR_END;  
 }    Revision 1.89  2003/06/24 12:30:52  brouard
     (Module): Some bugs corrected for windows. Also, when
 /******************free ivector **************************/    mle=-1 a template is output in file "or"mypar.txt with the design
 void free_ivector(int *v, long nl, long nh)    of the covariance matrix to be input.
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.88  2003/06/23 17:54:56  brouard
 }    * 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.
   
 /******************* imatrix *******************************/    Revision 1.87  2003/06/18 12:26:01  brouard
 int **imatrix(long nrl, long nrh, long ncl, long nch)    Version 0.96
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {    Revision 1.86  2003/06/17 20:04:08  brouard
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    (Module): Change position of html and gnuplot routines and added
   int **m;    routine fileappend.
    
   /* allocate pointers to rows */    Revision 1.85  2003/06/17 13:12:43  brouard
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    * imach.c (Repository): Check when date of death was earlier that
   if (!m) nrerror("allocation failure 1 in matrix()");    current date of interview. It may happen when the death was just
   m += NR_END;    prior to the death. In this case, dh was negative and likelihood
   m -= nrl;    was wrong (infinity). We still send an "Error" but patch by
      assuming that the date of death was just one stepm after the
      interview.
   /* allocate rows and set pointers to them */    (Repository): Because some people have very long ID (first column)
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    we changed int to long in num[] and we added a new lvector for
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    memory allocation. But we also truncated to 8 characters (left
   m[nrl] += NR_END;    truncation)
   m[nrl] -= ncl;    (Repository): No more line truncation errors.
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    Revision 1.84  2003/06/13 21:44:43  brouard
      * imach.c (Repository): Replace "freqsummary" at a correct
   /* return pointer to array of pointers to rows */    place. It differs from routine "prevalence" which may be called
   return m;    many times. Probs is memory consuming and must be used with
 }    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)    Revision 1.83  2003/06/10 13:39:11  lievre
       int **m;    *** empty log message ***
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */    Revision 1.82  2003/06/05 15:57:20  brouard
 {    Add log in  imach.c and  fullversion number is now printed.
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  */
 }  /*
      Interpolated Markov Chain
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    Short summary of the programme:
 {    
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    This program computes Healthy Life Expectancies from
   double **m;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    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
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    model. More health states you consider, more time is necessary to reach the
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    Maximum Likelihood of the parameters involved in the model.  The
   m[nrl] += NR_END;    simplest model is the multinomial logistic model where pij is the
   m[nrl] -= ncl;    probability to be observed in state j at the second wave
     conditional to be observed in state i at the first wave. Therefore
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   return m;    'age' is age and 'sex' is a covariate. If you want to have a more
 }    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
 /*************************free matrix ************************/    you to do it.  More covariates you add, slower the
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    convergence.
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    The advantage of this computer programme, compared to a simple
   free((FREE_ARG)(m+nrl-NR_END));    multinomial logistic model, is clear when the delay between waves is not
 }    identical for each individual. Also, if a individual missed an
     intermediate interview, the information is lost, but taken into
 /******************* ma3x *******************************/    account using an interpolation or extrapolation.  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {    hPijx is the probability to be observed in state i at age x+h
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    conditional to the observed state i at age x. The delay 'h' can be
   double ***m;    split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    semester or year) is modelled as a multinomial logistic.  The hPx
   if (!m) nrerror("allocation failure 1 in matrix()");    matrix is simply the matrix product of nh*stepm elementary matrices
   m += NR_END;    and the contribution of each individual to the likelihood is simply
   m -= nrl;    hPijx.
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    Also this programme outputs the covariance matrix of the parameters but also
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    of the life expectancies. It also computes the period (stable) prevalence. 
   m[nrl] += NR_END;    
   m[nrl] -= ncl;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    It is copyrighted identically to a GNU software product, ie programme and
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    software can be distributed freely for non commercial use. Latest version
   m[nrl][ncl] += NR_END;    can be accessed at http://euroreves.ined.fr/imach .
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     m[nrl][j]=m[nrl][j-1]+nlay;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
      
   for (i=nrl+1; i<=nrh; i++) {    **********************************************************************/
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  /*
     for (j=ncl+1; j<=nch; j++)    main
       m[i][j]=m[i][j-1]+nlay;    read parameterfile
   }    read datafile
   return m;    concatwav
 }    freqsummary
     if (mle >= 1)
 /*************************free ma3x ************************/      mlikeli
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    print results files
 {    if mle==1 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));       computes hessian
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    read end of parameter file: agemin, agemax, bage, fage, estepm
   free((FREE_ARG)(m+nrl-NR_END));        begin-prev-date,...
 }    open gnuplot file
     open html file
 /***************** f1dim *************************/    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
 extern int ncom;     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
 extern double *pcom,*xicom;                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
 extern double (*nrfunc)(double []);      freexexit2 possible for memory heap.
    
 double f1dim(double x)    h Pij x                         | pij_nom  ficrestpij
 {     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
   int j;         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
   double f;         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   double *xt;  
           1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
   xt=vector(1,ncom);         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
   f=(*nrfunc)(xt);     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
   free_vector(xt,1,ncom);     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
   return f;  
 }    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
 /*****************brent *************************/    Variance-covariance of DFLE
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    prevalence()
 {     movingaverage()
   int iter;    varevsij() 
   double a,b,d,etemp;    if popbased==1 varevsij(,popbased)
   double fu,fv,fw,fx;    total life expectancies
   double ftemp;    Variance of period (stable) prevalence
   double p,q,r,tol1,tol2,u,v,w,x,xm;   end
   double e=0.0;  */
    
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;   
   fw=fv=fx=(*f)(x);  #include <math.h>
   for (iter=1;iter<=ITMAX;iter++) {  #include <stdio.h>
     xm=0.5*(a+b);  #include <stdlib.h>
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  #include <string.h>
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  #include <unistd.h>
     printf(".");fflush(stdout);  
 #ifdef DEBUG  #include <limits.h>
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  #include <sys/types.h>
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  #include <sys/stat.h>
 #endif  #include <errno.h>
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  extern int errno;
       *xmin=x;  
       return fx;  #ifdef LINUX
     }  #include <time.h>
     ftemp=fu;  #include "timeval.h"
     if (fabs(e) > tol1) {  #else
       r=(x-w)*(fx-fv);  #include <sys/time.h>
       q=(x-v)*(fx-fw);  #endif
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);  #ifdef GSL
       if (q > 0.0) p = -p;  #include <gsl/gsl_errno.h>
       q=fabs(q);  #include <gsl/gsl_multimin.h>
       etemp=e;  #endif
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  /* #include <libintl.h> */
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  /* #define _(String) gettext (String) */
       else {  
         d=p/q;  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)  #define GNUPLOTPROGRAM "gnuplot"
           d=SIGN(tol1,xm-x);  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       }  #define FILENAMELENGTH 132
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
     }  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
     if (fu <= fx) {  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  #define NINTERVMAX 8
         SHFT(fv,fw,fx,fu)  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
         } else {  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
           if (u < x) a=u; else b=u;  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
           if (fu <= fw || w == x) {  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
             v=w;  #define MAXN 20000
             w=u;  #define YEARM 12. /**< Number of months per year */
             fv=fw;  #define AGESUP 130
             fw=fu;  #define AGEBASE 40
           } else if (fu <= fv || v == x || v == w) {  #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
             v=u;  #ifdef UNIX
             fv=fu;  #define DIRSEPARATOR '/'
           }  #define CHARSEPARATOR "/"
         }  #define ODIRSEPARATOR '\\'
   }  #else
   nrerror("Too many iterations in brent");  #define DIRSEPARATOR '\\'
   *xmin=x;  #define CHARSEPARATOR "\\"
   return fx;  #define ODIRSEPARATOR '/'
 }  #endif
   
 /****************** mnbrak ***********************/  /* $Id$ */
   /* $State$ */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))  char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
 {  char fullversion[]="$Revision$ $Date$"; 
   double ulim,u,r,q, dum;  char strstart[80];
   double fu;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
    int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   *fa=(*func)(*ax);  int nvar=0, nforce=0; /* Number of variables, number of forces */
   *fb=(*func)(*bx);  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   if (*fb > *fa) {  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
     SHFT(dum,*ax,*bx,dum)  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
       SHFT(dum,*fb,*fa,dum)  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
       }  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
   *cx=(*bx)+GOLD*(*bx-*ax);  int cptcovprodnoage=0; /**< Number of covariate products without age */   
   *fc=(*func)(*cx);  int cptcoveff=0; /* Total number of covariates to vary for printing results */
   while (*fb > *fc) {  int cptcov=0; /* Working variable */
     r=(*bx-*ax)*(*fb-*fc);  int npar=NPARMAX;
     q=(*bx-*cx)*(*fb-*fa);  int nlstate=2; /* Number of live states */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  int ndeath=1; /* Number of dead states */
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
     ulim=(*bx)+GLIMIT*(*cx-*bx);  int popbased=0;
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);  int *wav; /* Number of waves for this individuual 0 is possible */
     } else if ((*cx-u)*(u-ulim) > 0.0) {  int maxwav=0; /* Maxim number of waves */
       fu=(*func)(u);  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
       if (fu < *fc) {  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
           SHFT(*fb,*fc,fu,(*func)(u))                     to the likelihood and the sum of weights (done by funcone)*/
           }  int mle=1, weightopt=0;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       u=ulim;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       fu=(*func)(u);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     } else {             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       u=(*cx)+GOLD*(*cx-*bx);  double jmean=1; /* Mean space between 2 waves */
       fu=(*func)(u);  double **matprod2(); /* test */
     }  double **oldm, **newm, **savm; /* Working pointers to matrices */
     SHFT(*ax,*bx,*cx,u)  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       SHFT(*fa,*fb,*fc,fu)  /*FILE *fic ; */ /* Used in readdata only */
       }  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 }  FILE *ficlog, *ficrespow;
   int globpr=0; /* Global variable for printing or not */
 /*************** linmin ************************/  double fretone; /* Only one call to likelihood */
   long ipmx=0; /* Number of contributions */
 int ncom;  double sw; /* Sum of weights */
 double *pcom,*xicom;  char filerespow[FILENAMELENGTH];
 double (*nrfunc)(double []);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
    FILE *ficresilk;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 {  FILE *ficresprobmorprev;
   double brent(double ax, double bx, double cx,  FILE *fichtm, *fichtmcov; /* Html File */
                double (*f)(double), double tol, double *xmin);  FILE *ficreseij;
   double f1dim(double x);  char filerese[FILENAMELENGTH];
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  FILE *ficresstdeij;
               double *fc, double (*func)(double));  char fileresstde[FILENAMELENGTH];
   int j;  FILE *ficrescveij;
   double xx,xmin,bx,ax;  char filerescve[FILENAMELENGTH];
   double fx,fb,fa;  FILE  *ficresvij;
    char fileresv[FILENAMELENGTH];
   ncom=n;  FILE  *ficresvpl;
   pcom=vector(1,n);  char fileresvpl[FILENAMELENGTH];
   xicom=vector(1,n);  char title[MAXLINE];
   nrfunc=func;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   for (j=1;j<=n;j++) {  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     pcom[j]=p[j];  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     xicom[j]=xi[j];  char command[FILENAMELENGTH];
   }  int  outcmd=0;
   ax=0.0;  
   xx=1.0;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  char filelog[FILENAMELENGTH]; /* Log file */
 #ifdef DEBUG  char filerest[FILENAMELENGTH];
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  char fileregp[FILENAMELENGTH];
 #endif  char popfile[FILENAMELENGTH];
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     p[j] += xi[j];  
   }  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   free_vector(xicom,1,n);  struct timezone tzp;
   free_vector(pcom,1,n);  extern int gettimeofday();
 }  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   long time_value;
 /*************** powell ************************/  extern long time();
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  char strcurr[80], strfor[80];
             double (*func)(double []))  
 {  char *endptr;
   void linmin(double p[], double xi[], int n, double *fret,  long lval;
               double (*func)(double []));  double dval;
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;  #define NR_END 1
   double fp,fptt;  #define FREE_ARG char*
   double *xits;  #define FTOL 1.0e-10
   pt=vector(1,n);  
   ptt=vector(1,n);  #define NRANSI 
   xit=vector(1,n);  #define ITMAX 200 
   xits=vector(1,n);  
   *fret=(*func)(p);  #define TOL 2.0e-4 
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  #define CGOLD 0.3819660 
     fp=(*fret);  #define ZEPS 1.0e-10 
     ibig=0;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     del=0.0;  
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  #define GOLD 1.618034 
     for (i=1;i<=n;i++)  #define GLIMIT 100.0 
       printf(" %d %.12f",i, p[i]);  #define TINY 1.0e-20 
     printf("\n");  
     for (i=1;i<=n;i++) {  static double maxarg1,maxarg2;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       fptt=(*fret);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 #ifdef DEBUG    
       printf("fret=%lf \n",*fret);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 #endif  #define rint(a) floor(a+0.5)
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  static double sqrarg;
       if (fabs(fptt-(*fret)) > del) {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
         del=fabs(fptt-(*fret));  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
         ibig=i;  int agegomp= AGEGOMP;
       }  
 #ifdef DEBUG  int imx; 
       printf("%d %.12e",i,(*fret));  int stepm=1;
       for (j=1;j<=n;j++) {  /* Stepm, step in month: minimum step interpolation*/
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);  int estepm;
       }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       for(j=1;j<=n;j++)  
         printf(" p=%.12e",p[j]);  int m,nb;
       printf("\n");  long *num;
 #endif  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
     }  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  double **pmmij, ***probs;
 #ifdef DEBUG  double *ageexmed,*agecens;
       int k[2],l;  double dateintmean=0;
       k[0]=1;  
       k[1]=-1;  double *weight;
       printf("Max: %.12e",(*func)(p));  int **s; /* Status */
       for (j=1;j<=n;j++)  double *agedc;
         printf(" %.12e",p[j]);  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
       printf("\n");                    * covar=matrix(0,NCOVMAX,1,n); 
       for(l=0;l<=1;l++) {                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
         for (j=1;j<=n;j++) {  double  idx; 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  int *Ndum; /** Freq of modality (tricode */
         }  int **codtab; /**< codtab=imatrix(1,100,1,10); */
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
       }  double *lsurv, *lpop, *tpop;
 #endif  
   double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
   double ftolhess; /**< Tolerance for computing hessian */
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  /**************** split *************************/
       free_vector(ptt,1,n);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       free_vector(pt,1,n);  {
       return;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
     }       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    */ 
     for (j=1;j<=n;j++) {    char  *ss;                            /* pointer */
       ptt[j]=2.0*p[j]-pt[j];    int   l1, l2;                         /* length counters */
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];    l1 = strlen(path );                   /* length of path */
     }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     fptt=(*func)(ptt);    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if (fptt < fp) {    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      strcpy( name, path );               /* we got the fullname name because no directory */
       if (t < 0.0) {      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         linmin(p,xit,n,fret,func);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
         for (j=1;j<=n;j++) {      /* get current working directory */
           xi[j][ibig]=xi[j][n];      /*    extern  char* getcwd ( char *buf , int len);*/
           xi[j][n]=xit[j];      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         }        return( GLOCK_ERROR_GETCWD );
 #ifdef DEBUG      }
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      /* got dirc from getcwd*/
         for(j=1;j<=n;j++)      printf(" DIRC = %s \n",dirc);
           printf(" %.12e",xit[j]);    } else {                              /* strip direcotry from path */
         printf("\n");      ss++;                               /* after this, the filename */
 #endif      l2 = strlen( ss );                  /* length of filename */
       }      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     }      strcpy( name, ss );         /* save file name */
   }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 }      dirc[l1-l2] = 0;                    /* add zero */
       printf(" DIRC2 = %s \n",dirc);
 /**** Prevalence limit ****************/    }
     /* We add a separator at the end of dirc if not exists */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    l1 = strlen( dirc );                  /* length of directory */
 {    if( dirc[l1-1] != DIRSEPARATOR ){
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      dirc[l1] =  DIRSEPARATOR;
      matrix by transitions matrix until convergence is reached */      dirc[l1+1] = 0; 
       printf(" DIRC3 = %s \n",dirc);
   int i, ii,j,k;    }
   double min, max, maxmin, maxmax,sumnew=0.;    ss = strrchr( name, '.' );            /* find last / */
   double **matprod2();    if (ss >0){
   double **out, cov[NCOVMAX], **pmij();      ss++;
   double **newm;      strcpy(ext,ss);                     /* save extension */
   double agefin, delaymax=50 ; /* Max number of years to converge */      l1= strlen( name);
       l2= strlen(ss)+1;
   for (ii=1;ii<=nlstate+ndeath;ii++)      strncpy( finame, name, l1-l2);
     for (j=1;j<=nlstate+ndeath;j++){      finame[l1-l2]= 0;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    }
     }  
     return( 0 );                          /* we're done */
    cov[1]=1.;  }
    
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  /******************************************/
     newm=savm;  
     /* Covariates have to be included here again */  void replace_back_to_slash(char *s, char*t)
      cov[2]=agefin;  {
      int i;
       for (k=1; k<=cptcovn;k++) {    int lg=0;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    i=0;
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    lg=strlen(t);
       }    for(i=0; i<= lg; i++) {
       for (k=1; k<=cptcovage;k++)      (s[i] = t[i]);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      if (t[i]== '\\') s[i]='/';
       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]]];  }
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  char *trimbb(char *out, char *in)
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
     char *s;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    s=out;
     while (*in != '\0'){
     savm=oldm;      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
     oldm=newm;        in++;
     maxmax=0.;      }
     for(j=1;j<=nlstate;j++){      *out++ = *in++;
       min=1.;    }
       max=0.;    *out='\0';
       for(i=1; i<=nlstate; i++) {    return s;
         sumnew=0;  }
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  char *cutl(char *blocc, char *alocc, char *in, char occ)
         max=FMAX(max,prlim[i][j]);  {
         min=FMIN(min,prlim[i][j]);    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
       }       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       maxmin=max-min;       gives blocc="abcdef2ghi" and alocc="j".
       maxmax=FMAX(maxmax,maxmin);       If occ is not found blocc is null and alocc is equal to in. Returns blocc
     }    */
     if(maxmax < ftolpl){    char *s, *t, *bl;
       return prlim;    t=in;s=in;
     }    while ((*in != occ) && (*in != '\0')){
   }      *alocc++ = *in++;
 }    }
     if( *in == occ){
 /*************** transition probabilities ***************/      *(alocc)='\0';
       s=++in;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    }
 {   
   double s1, s2;    if (s == t) {/* occ not found */
   /*double t34;*/      *(alocc-(in-s))='\0';
   int i,j,j1, nc, ii, jj;      in=s;
     }
     for(i=1; i<= nlstate; i++){    while ( *in != '\0'){
     for(j=1; j<i;j++){      *blocc++ = *in++;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    }
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    *blocc='\0';
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    return t;
       }  }
       ps[i][j]=s2;  char *cutv(char *blocc, char *alocc, char *in, char occ)
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  {
     }    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
     for(j=i+1; j<=nlstate+ndeath;j++){       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){       gives blocc="abcdef2ghi" and alocc="j".
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];       If occ is not found blocc is null and alocc is equal to in. Returns alocc
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    */
       }    char *s, *t;
       ps[i][j]=s2;    t=in;s=in;
     }    while (*in != '\0'){
   }      while( *in == occ){
     /*ps[3][2]=1;*/        *blocc++ = *in++;
         s=in;
   for(i=1; i<= nlstate; i++){      }
      s1=0;      *blocc++ = *in++;
     for(j=1; j<i; j++)    }
       s1+=exp(ps[i][j]);    if (s == t) /* occ not found */
     for(j=i+1; j<=nlstate+ndeath; j++)      *(blocc-(in-s))='\0';
       s1+=exp(ps[i][j]);    else
     ps[i][i]=1./(s1+1.);      *(blocc-(in-s)-1)='\0';
     for(j=1; j<i; j++)    in=s;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    while ( *in != '\0'){
     for(j=i+1; j<=nlstate+ndeath; j++)      *alocc++ = *in++;
       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 */    *alocc='\0';
     return s;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  }
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;  int nbocc(char *s, char occ)
       ps[ii][ii]=1;  {
     }    int i,j=0;
   }    int lg=20;
     i=0;
     lg=strlen(s);
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    for(i=0; i<= lg; i++) {
     for(jj=1; jj<= nlstate+ndeath; jj++){    if  (s[i] == occ ) j++;
      printf("%lf ",ps[ii][jj]);    }
    }    return j;
     printf("\n ");  }
     }  
     printf("\n ");printf("%lf ",cov[2]);*/  /* void cutv(char *u,char *v, char*t, char occ) */
 /*  /* { */
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
   goto end;*/  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
     return ps;  /*      gives u="abcdef2ghi" and v="j" *\/ */
 }  /*   int i,lg,j,p=0; */
   /*   i=0; */
 /**************** Product of 2 matrices ******************/  /*   lg=strlen(t); */
   /*   for(j=0; j<=lg-1; j++) { */
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
 {  /*   } */
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  /*   for(j=0; j<p; j++) { */
   /* in, b, out are matrice of pointers which should have been initialized  /*     (u[j] = t[j]); */
      before: only the contents of out is modified. The function returns  /*   } */
      a pointer to pointers identical to out */  /*      u[p]='\0'; */
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)  /*    for(j=0; j<= lg; j++) { */
     for(k=ncolol; k<=ncoloh; k++)  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  /*   } */
         out[i][k] +=in[i][j]*b[j][k];  /* } */
   
   return out;  /********************** nrerror ********************/
 }  
   void nrerror(char error_text[])
   {
 /************* Higher Matrix Product ***************/    fprintf(stderr,"ERREUR ...\n");
     fprintf(stderr,"%s\n",error_text);
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    exit(EXIT_FAILURE);
 {  }
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  /*********************** vector *******************/
      duration (i.e. until  double *vector(int nl, int nh)
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  {
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    double *v;
      (typically every 2 years instead of every month which is too big).    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
      Model is determined by parameters x and covariates have to be    if (!v) nrerror("allocation failure in vector");
      included manually here.    return v-nl+NR_END;
   }
      */  
   /************************ free vector ******************/
   int i, j, d, h, k;  void free_vector(double*v, int nl, int nh)
   double **out, cov[NCOVMAX];  {
   double **newm;    free((FREE_ARG)(v+nl-NR_END));
   }
   /* Hstepm could be zero and should return the unit matrix */  
   for (i=1;i<=nlstate+ndeath;i++)  /************************ivector *******************************/
     for (j=1;j<=nlstate+ndeath;j++){  int *ivector(long nl,long nh)
       oldm[i][j]=(i==j ? 1.0 : 0.0);  {
       po[i][j][0]=(i==j ? 1.0 : 0.0);    int *v;
     }    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    if (!v) nrerror("allocation failure in ivector");
   for(h=1; h <=nhstepm; h++){    return v-nl+NR_END;
     for(d=1; d <=hstepm; d++){  }
       newm=savm;  
       /* Covariates have to be included here again */  /******************free ivector **************************/
       cov[1]=1.;  void free_ivector(int *v, long nl, long nh)
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  {
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    free((FREE_ARG)(v+nl-NR_END));
       for (k=1; k<=cptcovage;k++)  }
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  /************************lvector *******************************/
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  long *lvector(long nl,long nh)
   {
     long *v;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    if (!v) nrerror("allocation failure in ivector");
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    return v-nl+NR_END;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  }
       savm=oldm;  
       oldm=newm;  /******************free lvector **************************/
     }  void free_lvector(long *v, long nl, long nh)
     for(i=1; i<=nlstate+ndeath; i++)  {
       for(j=1;j<=nlstate+ndeath;j++) {    free((FREE_ARG)(v+nl-NR_END));
         po[i][j][h]=newm[i][j];  }
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  
          */  /******************* imatrix *******************************/
       }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   } /* end h */       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   return po;  { 
 }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     int **m; 
     
 /*************** log-likelihood *************/    /* allocate pointers to rows */ 
 double func( double *x)    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 {    if (!m) nrerror("allocation failure 1 in matrix()"); 
   int i, ii, j, k, mi, d, kk;    m += NR_END; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    m -= nrl; 
   double **out;    
   double sw; /* Sum of weights */    
   double lli; /* Individual log likelihood */    /* allocate rows and set pointers to them */ 
   long ipmx;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   /*extern weight */    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   /* We are differentiating ll according to initial status */    m[nrl] += NR_END; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    m[nrl] -= ncl; 
   /*for(i=1;i<imx;i++)    
     printf(" %d\n",s[4][i]);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   */    
   cov[1]=1.;    /* return pointer to array of pointers to rows */ 
     return m; 
   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];  /****************** free_imatrix *************************/
     for(mi=1; mi<= wav[i]-1; mi++){  void free_imatrix(m,nrl,nrh,ncl,nch)
       for (ii=1;ii<=nlstate+ndeath;ii++)        int **m;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        long nch,ncl,nrh,nrl; 
       for(d=0; d<dh[mi][i]; d++){       /* free an int matrix allocated by imatrix() */ 
         newm=savm;  { 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         for (kk=1; kk<=cptcovage;kk++) {    free((FREE_ARG) (m+nrl-NR_END)); 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  } 
         }  
          /******************* matrix *******************************/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  double **matrix(long nrl, long nrh, long ncl, long nch)
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  {
         savm=oldm;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         oldm=newm;    double **m;
          
            m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       } /* end mult */    if (!m) nrerror("allocation failure 1 in matrix()");
          m += NR_END;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    m -= nrl;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  
       ipmx +=1;    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       sw += weight[i];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    m[nrl] += NR_END;
     } /* end of wave */    m[nrl] -= ncl;
   } /* end of individual */  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    return m;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   return -l;  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
 }     */
   }
   
 /*********** Maximum Likelihood Estimation ***************/  /*************************free matrix ************************/
   void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  {
 {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   int i,j, iter;    free((FREE_ARG)(m+nrl-NR_END));
   double **xi,*delti;  }
   double fret;  
   xi=matrix(1,npar,1,npar);  /******************* ma3x *******************************/
   for (i=1;i<=npar;i++)  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     for (j=1;j<=npar;j++)  {
       xi[i][j]=(i==j ? 1.0 : 0.0);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   printf("Powell\n");    double ***m;
   powell(p,xi,npar,ftol,&iter,&fret,func);  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    if (!m) nrerror("allocation failure 1 in matrix()");
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    m += NR_END;
     m -= nrl;
 }  
     m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 /**** Computes Hessian and covariance matrix ***/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    m[nrl] += NR_END;
 {    m[nrl] -= ncl;
   double  **a,**y,*x,pd;  
   double **hess;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   int i, j,jk;  
   int *indx;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   double hessii(double p[], double delta, int theta, double delti[]);    m[nrl][ncl] += NR_END;
   double hessij(double p[], double delti[], int i, int j);    m[nrl][ncl] -= nll;
   void lubksb(double **a, int npar, int *indx, double b[]) ;    for (j=ncl+1; j<=nch; j++) 
   void ludcmp(double **a, int npar, int *indx, double *d) ;      m[nrl][j]=m[nrl][j-1]+nlay;
     
   hess=matrix(1,npar,1,npar);    for (i=nrl+1; i<=nrh; i++) {
       m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   printf("\nCalculation of the hessian matrix. Wait...\n");      for (j=ncl+1; j<=nch; j++) 
   for (i=1;i<=npar;i++){        m[i][j]=m[i][j-1]+nlay;
     printf("%d",i);fflush(stdout);    }
     hess[i][i]=hessii(p,ftolhess,i,delti);    return m; 
     /*printf(" %f ",p[i]);*/    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     /*printf(" %lf ",hess[i][i]);*/             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   }    */
    }
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++)  {  /*************************free ma3x ************************/
       if (j>i) {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
         printf(".%d%d",i,j);fflush(stdout);  {
         hess[i][j]=hessij(p,delti,i,j);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
         hess[j][i]=hess[i][j];        free((FREE_ARG)(m[nrl]+ncl-NR_END));
         /*printf(" %lf ",hess[i][j]);*/    free((FREE_ARG)(m+nrl-NR_END));
       }  }
     }  
   }  /*************** function subdirf ***********/
   printf("\n");  char *subdirf(char fileres[])
   {
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    /* Caution optionfilefiname is hidden */
      strcpy(tmpout,optionfilefiname);
   a=matrix(1,npar,1,npar);    strcat(tmpout,"/"); /* Add to the right */
   y=matrix(1,npar,1,npar);    strcat(tmpout,fileres);
   x=vector(1,npar);    return tmpout;
   indx=ivector(1,npar);  }
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  /*************** function subdirf2 ***********/
   ludcmp(a,npar,indx,&pd);  char *subdirf2(char fileres[], char *preop)
   {
   for (j=1;j<=npar;j++) {    
     for (i=1;i<=npar;i++) x[i]=0;    /* Caution optionfilefiname is hidden */
     x[j]=1;    strcpy(tmpout,optionfilefiname);
     lubksb(a,npar,indx,x);    strcat(tmpout,"/");
     for (i=1;i<=npar;i++){    strcat(tmpout,preop);
       matcov[i][j]=x[i];    strcat(tmpout,fileres);
     }    return tmpout;
   }  }
   
   printf("\n#Hessian matrix#\n");  /*************** function subdirf3 ***********/
   for (i=1;i<=npar;i++) {  char *subdirf3(char fileres[], char *preop, char *preop2)
     for (j=1;j<=npar;j++) {  {
       printf("%.3e ",hess[i][j]);    
     }    /* Caution optionfilefiname is hidden */
     printf("\n");    strcpy(tmpout,optionfilefiname);
   }    strcat(tmpout,"/");
     strcat(tmpout,preop);
   /* Recompute Inverse */    strcat(tmpout,preop2);
   for (i=1;i<=npar;i++)    strcat(tmpout,fileres);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    return tmpout;
   ludcmp(a,npar,indx,&pd);  }
   
   /*  printf("\n#Hessian matrix recomputed#\n");  /***************** f1dim *************************/
   extern int ncom; 
   for (j=1;j<=npar;j++) {  extern double *pcom,*xicom;
     for (i=1;i<=npar;i++) x[i]=0;  extern double (*nrfunc)(double []); 
     x[j]=1;   
     lubksb(a,npar,indx,x);  double f1dim(double x) 
     for (i=1;i<=npar;i++){  { 
       y[i][j]=x[i];    int j; 
       printf("%.3e ",y[i][j]);    double f;
     }    double *xt; 
     printf("\n");   
   }    xt=vector(1,ncom); 
   */    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
   free_matrix(a,1,npar,1,npar);    free_vector(xt,1,ncom); 
   free_matrix(y,1,npar,1,npar);    return f; 
   free_vector(x,1,npar);  } 
   free_ivector(indx,1,npar);  
   free_matrix(hess,1,npar,1,npar);  /*****************brent *************************/
   double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   { 
 }    int iter; 
     double a,b,d,etemp;
 /*************** hessian matrix ****************/    double fu,fv,fw,fx;
 double hessii( double x[], double delta, int theta, double delti[])    double ftemp;
 {    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   int i;    double e=0.0; 
   int l=1, lmax=20;   
   double k1,k2;    a=(ax < cx ? ax : cx); 
   double p2[NPARMAX+1];    b=(ax > cx ? ax : cx); 
   double res;    x=w=v=bx; 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    fw=fv=fx=(*f)(x); 
   double fx;    for (iter=1;iter<=ITMAX;iter++) { 
   int k=0,kmax=10;      xm=0.5*(a+b); 
   double l1;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   fx=func(x);      printf(".");fflush(stdout);
   for (i=1;i<=npar;i++) p2[i]=x[i];      fprintf(ficlog,".");fflush(ficlog);
   for(l=0 ; l <=lmax; l++){  #ifdef DEBUG
     l1=pow(10,l);      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);
     delts=delt;      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     for(k=1 ; k <kmax; k=k+1){      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       delt = delta*(l1*k);  #endif
       p2[theta]=x[theta] +delt;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       k1=func(p2)-fx;        *xmin=x; 
       p2[theta]=x[theta]-delt;        return fx; 
       k2=func(p2)-fx;      } 
       /*res= (k1-2.0*fx+k2)/delt/delt; */      ftemp=fu;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      if (fabs(e) > tol1) { 
              r=(x-w)*(fx-fv); 
 #ifdef DEBUG        q=(x-v)*(fx-fw); 
       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);        p=(x-v)*q-(x-w)*r; 
 #endif        q=2.0*(q-r); 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        if (q > 0.0) p = -p; 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        q=fabs(q); 
         k=kmax;        etemp=e; 
       }        e=d; 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         k=kmax; l=lmax*10.;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       }        else { 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          d=p/q; 
         delts=delt;          u=x+d; 
       }          if (u-a < tol2 || b-u < tol2) 
     }            d=SIGN(tol1,xm-x); 
   }        } 
   delti[theta]=delts;      } else { 
   return res;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
        } 
 }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       fu=(*f)(u); 
 double hessij( double x[], double delti[], int thetai,int thetaj)      if (fu <= fx) { 
 {        if (u >= x) a=x; else b=x; 
   int i;        SHFT(v,w,x,u) 
   int l=1, l1, lmax=20;          SHFT(fv,fw,fx,fu) 
   double k1,k2,k3,k4,res,fx;          } else { 
   double p2[NPARMAX+1];            if (u < x) a=u; else b=u; 
   int k;            if (fu <= fw || w == x) { 
               v=w; 
   fx=func(x);              w=u; 
   for (k=1; k<=2; k++) {              fv=fw; 
     for (i=1;i<=npar;i++) p2[i]=x[i];              fw=fu; 
     p2[thetai]=x[thetai]+delti[thetai]/k;            } else if (fu <= fv || v == x || v == w) { 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;              v=u; 
     k1=func(p2)-fx;              fv=fu; 
              } 
     p2[thetai]=x[thetai]+delti[thetai]/k;          } 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    } 
     k2=func(p2)-fx;    nrerror("Too many iterations in brent"); 
      *xmin=x; 
     p2[thetai]=x[thetai]-delti[thetai]/k;    return fx; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  } 
     k3=func(p2)-fx;  
    /****************** mnbrak ***********************/
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     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    double ulim,u,r,q, dum;
     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 fu; 
 #endif   
   }    *fa=(*func)(*ax); 
   return res;    *fb=(*func)(*bx); 
 }    if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
 /************** Inverse of matrix **************/        SHFT(dum,*fb,*fa,dum) 
 void ludcmp(double **a, int n, int *indx, double *d)        } 
 {    *cx=(*bx)+GOLD*(*bx-*ax); 
   int i,imax,j,k;    *fc=(*func)(*cx); 
   double big,dum,sum,temp;    while (*fb > *fc) { 
   double *vv;      r=(*bx-*ax)*(*fb-*fc); 
        q=(*bx-*cx)*(*fb-*fa); 
   vv=vector(1,n);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   *d=1.0;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   for (i=1;i<=n;i++) {      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     big=0.0;      if ((*bx-u)*(u-*cx) > 0.0) { 
     for (j=1;j<=n;j++)        fu=(*func)(u); 
       if ((temp=fabs(a[i][j])) > big) big=temp;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        fu=(*func)(u); 
     vv[i]=1.0/big;        if (fu < *fc) { 
   }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   for (j=1;j<=n;j++) {            SHFT(*fb,*fc,fu,(*func)(u)) 
     for (i=1;i<j;i++) {            } 
       sum=a[i][j];      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        u=ulim; 
       a[i][j]=sum;        fu=(*func)(u); 
     }      } else { 
     big=0.0;        u=(*cx)+GOLD*(*cx-*bx); 
     for (i=j;i<=n;i++) {        fu=(*func)(u); 
       sum=a[i][j];      } 
       for (k=1;k<j;k++)      SHFT(*ax,*bx,*cx,u) 
         sum -= a[i][k]*a[k][j];        SHFT(*fa,*fb,*fc,fu) 
       a[i][j]=sum;        } 
       if ( (dum=vv[i]*fabs(sum)) >= big) {  } 
         big=dum;  
         imax=i;  /*************** linmin ************************/
       }  
     }  int ncom; 
     if (j != imax) {  double *pcom,*xicom;
       for (k=1;k<=n;k++) {  double (*nrfunc)(double []); 
         dum=a[imax][k];   
         a[imax][k]=a[j][k];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         a[j][k]=dum;  { 
       }    double brent(double ax, double bx, double cx, 
       *d = -(*d);                 double (*f)(double), double tol, double *xmin); 
       vv[imax]=vv[j];    double f1dim(double x); 
     }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     indx[j]=imax;                double *fc, double (*func)(double)); 
     if (a[j][j] == 0.0) a[j][j]=TINY;    int j; 
     if (j != n) {    double xx,xmin,bx,ax; 
       dum=1.0/(a[j][j]);    double fx,fb,fa;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;   
     }    ncom=n; 
   }    pcom=vector(1,n); 
   free_vector(vv,1,n);  /* Doesn't work */    xicom=vector(1,n); 
 ;    nrfunc=func; 
 }    for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
 void lubksb(double **a, int n, int *indx, double b[])      xicom[j]=xi[j]; 
 {    } 
   int i,ii=0,ip,j;    ax=0.0; 
   double sum;    xx=1.0; 
      mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   for (i=1;i<=n;i++) {    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     ip=indx[i];  #ifdef DEBUG
     sum=b[ip];    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     b[ip]=b[i];    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     if (ii)  #endif
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    for (j=1;j<=n;j++) { 
     else if (sum) ii=i;      xi[j] *= xmin; 
     b[i]=sum;      p[j] += xi[j]; 
   }    } 
   for (i=n;i>=1;i--) {    free_vector(xicom,1,n); 
     sum=b[i];    free_vector(pcom,1,n); 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  } 
     b[i]=sum/a[i][i];  
   }  char *asc_diff_time(long time_sec, char ascdiff[])
 }  {
     long sec_left, days, hours, minutes;
 /************ Frequencies ********************/    days = (time_sec) / (60*60*24);
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)    sec_left = (time_sec) % (60*60*24);
 {  /* Some frequencies */    hours = (sec_left) / (60*60) ;
      sec_left = (sec_left) %(60*60);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    minutes = (sec_left) /60;
   double ***freq; /* Frequencies */    sec_left = (sec_left) % (60);
   double *pp;    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
   double pos, k2, dateintsum=0,k2cpt=0;    return ascdiff;
   FILE *ficresp;  }
   char fileresp[FILENAMELENGTH];  
    /*************** powell ************************/
   pp=vector(1,nlstate);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);              double (*func)(double [])) 
   strcpy(fileresp,"p");  { 
   strcat(fileresp,fileres);    void linmin(double p[], double xi[], int n, double *fret, 
   if((ficresp=fopen(fileresp,"w"))==NULL) {                double (*func)(double [])); 
     printf("Problem with prevalence resultfile: %s\n", fileresp);    int i,ibig,j; 
     exit(0);    double del,t,*pt,*ptt,*xit;
   }    double fp,fptt;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    double *xits;
   j1=0;    int niterf, itmp;
   
   j=cptcoveff;    pt=vector(1,n); 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    ptt=vector(1,n); 
     xit=vector(1,n); 
   for(k1=1; k1<=j;k1++){    xits=vector(1,n); 
    for(i1=1; i1<=ncodemax[k1];i1++){    *fret=(*func)(p); 
        j1++;    for (j=1;j<=n;j++) pt[j]=p[j]; 
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    for (*iter=1;;++(*iter)) { 
          scanf("%d", i);*/      fp=(*fret); 
         for (i=-1; i<=nlstate+ndeath; i++)        ibig=0; 
          for (jk=-1; jk<=nlstate+ndeath; jk++)        del=0.0; 
            for(m=agemin; m <= agemax+3; m++)      last_time=curr_time;
              freq[i][jk][m]=0;      (void) gettimeofday(&curr_time,&tzp);
       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);
         dateintsum=0;      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);
         k2cpt=0;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
        for (i=1; i<=imx; i++) {     for (i=1;i<=n;i++) {
          bool=1;        printf(" %d %.12f",i, p[i]);
          if  (cptcovn>0) {        fprintf(ficlog," %d %.12lf",i, p[i]);
            for (z1=1; z1<=cptcoveff; z1++)        fprintf(ficrespow," %.12lf", p[i]);
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      }
                bool=0;      printf("\n");
          }      fprintf(ficlog,"\n");
          if (bool==1) {      fprintf(ficrespow,"\n");fflush(ficrespow);
            for(m=firstpass; m<=lastpass; m++){      if(*iter <=3){
              k2=anint[m][i]+(mint[m][i]/12.);        tm = *localtime(&curr_time.tv_sec);
              if ((k2>=dateprev1) && (k2<=dateprev2)) {        strcpy(strcurr,asctime(&tm));
                if(agev[m][i]==0) agev[m][i]=agemax+1;  /*       asctime_r(&tm,strcurr); */
                if(agev[m][i]==1) agev[m][i]=agemax+2;        forecast_time=curr_time; 
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        itmp = strlen(strcurr);
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          strcurr[itmp-1]='\0';
                  dateintsum=dateintsum+k2;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
                  k2cpt++;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
                }        for(niterf=10;niterf<=30;niterf+=10){
           forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
              }          tmf = *localtime(&forecast_time.tv_sec);
            }  /*      asctime_r(&tmf,strfor); */
          }          strcpy(strfor,asctime(&tmf));
        }          itmp = strlen(strfor);
                  if(strfor[itmp-1]=='\n')
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          strfor[itmp-1]='\0';
           printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
         if  (cptcovn>0) {          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);
          fprintf(ficresp, "\n#********** Variable ");        }
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      }
        fprintf(ficresp, "**********\n#");      for (i=1;i<=n;i++) { 
         }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
        for(i=1; i<=nlstate;i++)        fptt=(*fret); 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  #ifdef DEBUG
        fprintf(ficresp, "\n");        printf("fret=%lf \n",*fret);
                fprintf(ficlog,"fret=%lf \n",*fret);
   for(i=(int)agemin; i <= (int)agemax+3; i++){  #endif
     if(i==(int)agemax+3)        printf("%d",i);fflush(stdout);
       printf("Total");        fprintf(ficlog,"%d",i);fflush(ficlog);
     else        linmin(p,xit,n,fret,func); 
       printf("Age %d", i);        if (fabs(fptt-(*fret)) > del) { 
     for(jk=1; jk <=nlstate ; jk++){          del=fabs(fptt-(*fret)); 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          ibig=i; 
         pp[jk] += freq[jk][m][i];        } 
     }  #ifdef DEBUG
     for(jk=1; jk <=nlstate ; jk++){        printf("%d %.12e",i,(*fret));
       for(m=-1, pos=0; m <=0 ; m++)        fprintf(ficlog,"%d %.12e",i,(*fret));
         pos += freq[jk][m][i];        for (j=1;j<=n;j++) {
       if(pp[jk]>=1.e-10)          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          printf(" x(%d)=%.12e",j,xit[j]);
       else          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        }
     }        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
      for(jk=1; jk <=nlstate ; jk++){          fprintf(ficlog," p=%.12e",p[j]);
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        }
         pp[jk] += freq[jk][m][i];        printf("\n");
      }        fprintf(ficlog,"\n");
   #endif
     for(jk=1,pos=0; jk <=nlstate ; jk++)      } 
       pos += pp[jk];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     for(jk=1; jk <=nlstate ; jk++){  #ifdef DEBUG
       if(pos>=1.e-5)        int k[2],l;
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        k[0]=1;
       else        k[1]=-1;
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        printf("Max: %.12e",(*func)(p));
       if( i <= (int) agemax){        fprintf(ficlog,"Max: %.12e",(*func)(p));
         if(pos>=1.e-5){        for (j=1;j<=n;j++) {
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          printf(" %.12e",p[j]);
           probs[i][jk][j1]= pp[jk]/pos;          fprintf(ficlog," %.12e",p[j]);
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        }
         }        printf("\n");
       else        fprintf(ficlog,"\n");
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        for(l=0;l<=1;l++) {
       }          for (j=1;j<=n;j++) {
     }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     for(jk=-1; jk <=nlstate+ndeath; jk++)            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       for(m=-1; m <=nlstate+ndeath; m++)            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          }
     if(i <= (int) agemax)          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       fprintf(ficresp,"\n");          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     printf("\n");        }
     }  #endif
     }  
  }  
   dateintmean=dateintsum/k2cpt;        free_vector(xit,1,n); 
          free_vector(xits,1,n); 
   fclose(ficresp);        free_vector(ptt,1,n); 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        free_vector(pt,1,n); 
   free_vector(pp,1,nlstate);        return; 
       } 
   /* End of Freq */      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 }      for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
 /************ Prevalence ********************/        xit[j]=p[j]-pt[j]; 
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)        pt[j]=p[j]; 
 {  /* Some frequencies */      } 
        fptt=(*func)(ptt); 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      if (fptt < fp) { 
   double ***freq; /* Frequencies */        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   double *pp;        if (t < 0.0) { 
   double pos, k2;          linmin(p,xit,n,fret,func); 
           for (j=1;j<=n;j++) { 
   pp=vector(1,nlstate);            xi[j][ibig]=xi[j][n]; 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            xi[j][n]=xit[j]; 
            }
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  #ifdef DEBUG
   j1=0;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
            fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   j=cptcoveff;          for(j=1;j<=n;j++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            printf(" %.12e",xit[j]);
              fprintf(ficlog," %.12e",xit[j]);
  for(k1=1; k1<=j;k1++){          }
     for(i1=1; i1<=ncodemax[k1];i1++){          printf("\n");
       j1++;          fprintf(ficlog,"\n");
    #endif
       for (i=-1; i<=nlstate+ndeath; i++)          }
         for (jk=-1; jk<=nlstate+ndeath; jk++)        } 
           for(m=agemin; m <= agemax+3; m++)    } 
             freq[i][jk][m]=0;  } 
        
       for (i=1; i<=imx; i++) {  /**** Prevalence limit (stable or period prevalence)  ****************/
         bool=1;  
         if  (cptcovn>0) {  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
           for (z1=1; z1<=cptcoveff; z1++)  {
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
               bool=0;       matrix by transitions matrix until convergence is reached */
         }  
         if (bool==1) {    int i, ii,j,k;
           for(m=firstpass; m<=lastpass; m++){    double min, max, maxmin, maxmax,sumnew=0.;
             k2=anint[m][i]+(mint[m][i]/12.);    /* double **matprod2(); */ /* test */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    double **out, cov[NCOVMAX+1], **pmij();
               if(agev[m][i]==0) agev[m][i]=agemax+1;    double **newm;
               if(agev[m][i]==1) agev[m][i]=agemax+2;    double agefin, delaymax=50 ; /* Max number of years to converge */
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];  
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */    for (ii=1;ii<=nlstate+ndeath;ii++)
             }      for (j=1;j<=nlstate+ndeath;j++){
           }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }      }
       }  
         for(i=(int)agemin; i <= (int)agemax+3; i++){     cov[1]=1.;
           for(jk=1; jk <=nlstate ; jk++){   
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
               pp[jk] += freq[jk][m][i];    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
           }      newm=savm;
           for(jk=1; jk <=nlstate ; jk++){      /* Covariates have to be included here again */
             for(m=-1, pos=0; m <=0 ; m++)      cov[2]=agefin;
             pos += freq[jk][m][i];      
         }      for (k=1; k<=cptcovn;k++) {
                cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
          for(jk=1; jk <=nlstate ; jk++){        /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      }
              pp[jk] += freq[jk][m][i];      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
          }      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
                /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
          for(jk=1; jk <=nlstate ; 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){      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
                probs[i][jk][j1]= pp[jk]/pos;      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
              }      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
            }      
          }      savm=oldm;
                oldm=newm;
         }      maxmax=0.;
     }      for(j=1;j<=nlstate;j++){
   }        min=1.;
          max=0.;
          for(i=1; i<=nlstate; i++) {
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          sumnew=0;
   free_vector(pp,1,nlstate);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
            prlim[i][j]= newm[i][j]/(1-sumnew);
 }  /* End of Freq */          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
           max=FMAX(max,prlim[i][j]);
 /************* Waves Concatenation ***************/          min=FMIN(min,prlim[i][j]);
         }
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        maxmin=max-min;
 {        maxmax=FMAX(maxmax,maxmin);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      }
      Death is a valid wave (if date is known).      if(maxmax < ftolpl){
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        return prlim;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      }
      and mw[mi+1][i]. dh depends on stepm.    }
      */  }
   
   int i, mi, m;  /*************** transition probabilities ***************/ 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  
      double sum=0., jmean=0.;*/  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
   int j, k=0,jk, ju, jl;    /* According to parameters values stored in x and the covariate's values stored in cov,
   double sum=0.;       computes the probability to be observed in state j being in state i by appying the
   jmin=1e+5;       model to the ncovmodel covariates (including constant and age).
   jmax=-1;       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
   jmean=0.;       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
   for(i=1; i<=imx; i++){       ncth covariate in the global vector x is given by the formula:
     mi=0;       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
     m=firstpass;       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
     while(s[m][i] <= nlstate){       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
       if(s[m][i]>=1)       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
         mw[++mi][i]=m;       Outputs ps[i][j] the probability to be observed in j being in j according to
       if(m >=lastpass)       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
         break;    */
       else    double s1, lnpijopii;
         m++;    /*double t34;*/
     }/* end while */    int i,j,j1, nc, ii, jj;
     if (s[m][i] > nlstate){  
       mi++;     /* Death is another wave */      for(i=1; i<= nlstate; i++){
       /* if(mi==0)  never been interviewed correctly before death */        for(j=1; j<i;j++){
          /* Only death is a correct wave */          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       mw[mi][i]=m;            /*lnpijopii += param[i][j][nc]*cov[nc];*/
     }            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
   /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     wav[i]=mi;          }
     if(mi==0)          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
   }        }
         for(j=i+1; j<=nlstate+ndeath;j++){
   for(i=1; i<=imx; i++){          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
     for(mi=1; mi<wav[i];mi++){            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
       if (stepm <=0)            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
         dh[mi][i]=1;  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
       else{          }
         if (s[mw[mi+1][i]][i] > nlstate) {          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
           if (agedc[i] < 2*AGESUP) {        }
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      }
           if(j==0) j=1;  /* Survives at least one month after exam */      
           k=k+1;      for(i=1; i<= nlstate; i++){
           if (j >= jmax) jmax=j;        s1=0;
           if (j <= jmin) jmin=j;        for(j=1; j<i; j++){
           sum=sum+j;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
           /*if (j<0) printf("j=%d num=%d \n",j,i); */          /*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++){
         else{          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           k=k+1;        }
           if (j >= jmax) jmax=j;        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
           else if (j <= jmin)jmin=j;        ps[i][i]=1./(s1+1.);
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        /* Computing other pijs */
           sum=sum+j;        for(j=1; j<i; j++)
         }          ps[i][j]= exp(ps[i][j])*ps[i][i];
         jk= j/stepm;        for(j=i+1; j<=nlstate+ndeath; j++)
         jl= j -jk*stepm;          ps[i][j]= exp(ps[i][j])*ps[i][i];
         ju= j -(jk+1)*stepm;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         if(jl <= -ju)      } /* end i */
           dh[mi][i]=jk;      
         else      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
           dh[mi][i]=jk+1;        for(jj=1; jj<= nlstate+ndeath; jj++){
         if(dh[mi][i]==0)          ps[ii][jj]=0;
           dh[mi][i]=1; /* At least one step */          ps[ii][ii]=1;
       }        }
     }      }
   }      
   jmean=sum/k;      
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
  }      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
 /*********** Tricode ****************************/      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
 void tricode(int *Tvar, int **nbcode, int imx)      /*   } */
 {      /*   printf("\n "); */
   int Ndum[20],ij=1, k, j, i;      /* } */
   int cptcode=0;      /* printf("\n ");printf("%lf ",cov[2]);*/
   cptcoveff=0;      /*
          for(i=1; i<= npar; i++) printf("%f ",x[i]);
   for (k=0; k<19; k++) Ndum[k]=0;        goto end;*/
   for (k=1; k<=7; k++) ncodemax[k]=0;      return ps;
   }
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  
     for (i=1; i<=imx; i++) {  /**************** Product of 2 matrices ******************/
       ij=(int)(covar[Tvar[j]][i]);  
       Ndum[ij]++;  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  {
       if (ij > cptcode) cptcode=ij;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     }       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
     for (i=0; i<=cptcode; i++) {       before: only the contents of out is modified. The function returns
       if(Ndum[i]!=0) ncodemax[j]++;       a pointer to pointers identical to out */
     }    int i, j, k;
     ij=1;    for(i=nrl; i<= nrh; i++)
       for(k=ncolol; k<=ncoloh; k++){
         out[i][k]=0.;
     for (i=1; i<=ncodemax[j]; i++) {        for(j=ncl; j<=nch; j++)
       for (k=0; k<=19; k++) {          out[i][k] +=in[i][j]*b[j][k];
         if (Ndum[k] != 0) {      }
           nbcode[Tvar[j]][ij]=k;    return out;
           ij++;  }
         }  
         if (ij > ncodemax[j]) break;  
       }    /************* Higher Matrix Product ***************/
     }  
   }    double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   {
  for (k=0; k<19; k++) Ndum[k]=0;    /* Computes the transition matrix starting at age 'age' over 
        'nhstepm*hstepm*stepm' months (i.e. until
  for (i=1; i<=ncovmodel-2; i++) {       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       ij=Tvar[i];       nhstepm*hstepm matrices. 
       Ndum[ij]++;       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 the memory).
  ij=1;       Model is determined by parameters x and covariates have to be 
  for (i=1; i<=10; i++) {       included manually here. 
    if((Ndum[i]!=0) && (i<=ncov)){  
      Tvaraff[ij]=i;       */
      ij++;  
    }    int i, j, d, h, k;
  }    double **out, cov[NCOVMAX+1];
      double **newm;
     cptcoveff=ij-1;  
 }    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
 /*********** Health Expectancies ****************/      for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        po[i][j][0]=(i==j ? 1.0 : 0.0);
 {      }
   /* Health expectancies */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   int i, j, nhstepm, hstepm, h;    for(h=1; h <=nhstepm; h++){
   double age, agelim,hf;      for(d=1; d <=hstepm; d++){
   double ***p3mat;        newm=savm;
          /* Covariates have to be included here again */
   fprintf(ficreseij,"# Health expectancies\n");        cov[1]=1.;
   fprintf(ficreseij,"# Age");        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   for(i=1; i<=nlstate;i++)        for (k=1; k<=cptcovn;k++) 
     for(j=1; j<=nlstate;j++)          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       fprintf(ficreseij," %1d-%1d",i,j);        for (k=1; k<=cptcovage;k++)
   fprintf(ficreseij,"\n");          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
   hstepm=1*YEARM; /*  Every j years of age (in month) */          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   
   agelim=AGESUP;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     /* nhstepm age range expressed in number of stepm */        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     /* Typically if 20 years = 20*12/6=40 stepm */        savm=oldm;
     /*if (stepm >= YEARM) hstepm=1;*/        oldm=newm;
 hstepm=1;      }
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */      for(i=1; i<=nlstate+ndeath; i++)
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(j=1;j<=nlstate+ndeath;j++) {
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          po[i][j][h]=newm[i][j];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          }
 hf=stepm/YEARM;      /*printf("h=%d ",h);*/
 /*printf("stepm=%d nhstepm=%d hstepm=%d age=%lf ",stepm, nhstepm, hstepm, age);*/    } /* end h */
     for(i=1; i<=nlstate;i++)  /*     printf("\n H=%d \n",h); */
       for(j=1; j<=nlstate;j++)    return po;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){  }
           eij[i][j][(int)age] +=hf*(p3mat[i][j][h]+p3mat[i][j][h+1])/2.0;  
         }  
      /*************** log-likelihood *************/
     /* hf=1;  double func( double *x)
        if (stepm >= YEARM) hf=stepm/YEARM;*/  {
 hf=stepm/YEARM;    int i, ii, j, k, mi, d, kk;
      double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     fprintf(ficreseij,"%3.0f",age );    double **out;
     for(i=1; i<=nlstate;i++)    double sw; /* Sum of weights */
       for(j=1; j<=nlstate;j++){    double lli; /* Individual log likelihood */
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);    int s1, s2;
       }    double bbh, survp;
     fprintf(ficreseij,"\n");    long ipmx;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*extern weight */
   }    /* We are differentiating ll according to initial status */
 }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
 /************ Variance ******************/      printf(" %d\n",s[4][i]);
 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)    */
 {    cov[1]=1.;
   /* Variance of health expectancies */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    for(k=1; k<=nlstate; k++) ll[k]=0.;
   double **newm;  
   double **dnewm,**doldm;    if(mle==1){
   int i, j, nhstepm, hstepm, h;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int k, cptcode;        /* Computes the values of the ncovmodel covariates of the model
   double *xp;           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
   double **gp, **gm;           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
   double ***gradg, ***trgradg;           to be observed in j being in i according to the model.
   double ***p3mat;         */
   double age,agelim;        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
   int theta;          cov[2+k]=covar[Tvar[k]][i];
         }
    fprintf(ficresvij,"# Covariances of life expectancies\n");        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
   fprintf(ficresvij,"# Age");           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
   for(i=1; i<=nlstate;i++)           has been calculated etc */
     for(j=1; j<=nlstate;j++)        for(mi=1; mi<= wav[i]-1; mi++){
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          for (ii=1;ii<=nlstate+ndeath;ii++)
   fprintf(ficresvij,"\n");            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   xp=vector(1,npar);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   dnewm=matrix(1,nlstate,1,npar);            }
   doldm=matrix(1,nlstate,1,nlstate);          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
   hstepm=1*YEARM; /* Every year of age */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            for (kk=1; kk<=cptcovage;kk++) {
   agelim = AGESUP;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     if (stepm >= YEARM) hstepm=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            savm=oldm;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            oldm=newm;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          } /* end mult */
     gp=matrix(0,nhstepm,1,nlstate);        
     gm=matrix(0,nhstepm,1,nlstate);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias at large stepm.
     for(theta=1; theta <=npar; theta++){           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       for(i=1; i<=npar; i++){ /* Computes gradient */           * (in months) between two waves is not a multiple of stepm, we rounded to 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);           * the nearest (and in case of equal distance, to the lowest) interval but now
       }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);             * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);           * 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
       if (popbased==1) {           * -stepm/2 to stepm/2 .
         for(i=1; i<=nlstate;i++)           * For stepm=1 the results are the same as for previous versions of Imach.
           prlim[i][i]=probs[(int)age][i][ij];           * For stepm > 1 the results are less biased than in previous versions. 
       }           */
            s1=s[mw[mi][i]][i];
       for(j=1; j<= nlstate; j++){          s2=s[mw[mi+1][i]][i];
         for(h=0; h<=nhstepm; h++){          bbh=(double)bh[mi][i]/(double)stepm; 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          /* bias bh is positive if real duration
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];           * is higher than the multiple of stepm and negative otherwise.
         }           */
       }          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
              if( s2 > nlstate){ 
       for(i=1; i<=npar; i++) /* Computes gradient */            /* i.e. if s2 is a death state and if the date of death is known 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);               then the contribution to the likelihood is the probability to 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                 die between last step unit time and current  step unit time, 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);               which is also equal to probability to die before dh 
                 minus probability to die before dh-stepm . 
       if (popbased==1) {               In version up to 0.92 likelihood was computed
         for(i=1; i<=nlstate;i++)          as if date of death was unknown. Death was treated as any other
           prlim[i][i]=probs[(int)age][i][ij];          health state: the date of the interview describes the actual state
       }          and not the date of a change in health state. The former idea was
           to consider that at each interview the state was recorded
       for(j=1; j<= nlstate; j++){          (healthy, disable or death) and IMaCh was corrected; but when we
         for(h=0; h<=nhstepm; h++){          introduced the exact date of death then we should have modified
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          the contribution of an exact death to the likelihood. This new
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          contribution is smaller and very dependent of the step unit
         }          stepm. It is no more the probability to die between last interview
       }          and month of death but the probability to survive from last
           interview up to one month before death multiplied by the
       for(j=1; j<= nlstate; j++)          probability to die within a month. Thanks to Chris
         for(h=0; h<=nhstepm; h++){          Jackson for correcting this bug.  Former versions increased
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          mortality artificially. The bad side is that we add another loop
         }          which slows down the processing. The difference can be up to 10%
     } /* End theta */          lower mortality.
             */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            lli=log(out[s1][s2] - savm[s1][s2]);
   
     for(h=0; h<=nhstepm; h++)  
       for(j=1; j<=nlstate;j++)          } else if  (s2==-2) {
         for(theta=1; theta <=npar; theta++)            for (j=1,survp=0. ; j<=nlstate; j++) 
           trgradg[h][j][theta]=gradg[h][theta][j];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             /*survp += out[s1][j]; */
     for(i=1;i<=nlstate;i++)            lli= log(survp);
       for(j=1;j<=nlstate;j++)          }
         vareij[i][j][(int)age] =0.;          
     for(h=0;h<=nhstepm;h++){          else if  (s2==-4) { 
       for(k=0;k<=nhstepm;k++){            for (j=3,survp=0. ; j<=nlstate; j++)  
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            lli= log(survp); 
         for(i=1;i<=nlstate;i++)          } 
           for(j=1;j<=nlstate;j++)  
             vareij[i][j][(int)age] += doldm[i][j];          else if  (s2==-5) { 
       }            for (j=1,survp=0. ; j<=2; j++)  
     }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     h=1;            lli= log(survp); 
     if (stepm >= YEARM) h=stepm/YEARM;          } 
     fprintf(ficresvij,"%.0f ",age );          
     for(i=1; i<=nlstate;i++)          else{
       for(j=1; j<=nlstate;j++){            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
       }          } 
     fprintf(ficresvij,"\n");          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     free_matrix(gp,0,nhstepm,1,nlstate);          /*if(lli ==000.0)*/
     free_matrix(gm,0,nhstepm,1,nlstate);          /*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); */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          ipmx +=1;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          sw += weight[i];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   } /* End age */        } /* end of wave */
        } /* end of individual */
   free_vector(xp,1,npar);    }  else if(mle==2){
   free_matrix(doldm,1,nlstate,1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_matrix(dnewm,1,nlstate,1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
 }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
 /************ Variance of prevlim ******************/              oldm[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)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 {            }
   /* Variance of prevalence limit */          for(d=0; d<=dh[mi][i]; d++){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            newm=savm;
   double **newm;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double **dnewm,**doldm;            for (kk=1; kk<=cptcovage;kk++) {
   int i, j, nhstepm, hstepm;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   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++)          bbh=(double)bh[mi][i]/(double)stepm; 
       fprintf(ficresvpl," %1d-%1d",i,i);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   fprintf(ficresvpl,"\n");          ipmx +=1;
           sw += weight[i];
   xp=vector(1,npar);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   dnewm=matrix(1,nlstate,1,npar);        } /* end of wave */
   doldm=matrix(1,nlstate,1,nlstate);      } /* end of individual */
      }  else if(mle==3){  /* exponential inter-extrapolation */
   hstepm=1*YEARM; /* Every year of age */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   agelim = AGESUP;        for(mi=1; mi<= wav[i]-1; mi++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          for (ii=1;ii<=nlstate+ndeath;ii++)
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            for (j=1;j<=nlstate+ndeath;j++){
     if (stepm >= YEARM) hstepm=1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     gradg=matrix(1,npar,1,nlstate);            }
     gp=vector(1,nlstate);          for(d=0; d<dh[mi][i]; d++){
     gm=vector(1,nlstate);            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(theta=1; theta <=npar; theta++){            for (kk=1; kk<=cptcovage;kk++) {
       for(i=1; i<=npar; i++){ /* Computes gradient */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            }
       }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(i=1;i<=nlstate;i++)            savm=oldm;
         gp[i] = prlim[i][i];            oldm=newm;
              } /* end mult */
       for(i=1; i<=npar; i++) /* Computes gradient */        
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          s1=s[mw[mi][i]][i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          s2=s[mw[mi+1][i]][i];
       for(i=1;i<=nlstate;i++)          bbh=(double)bh[mi][i]/(double)stepm; 
         gm[i] = prlim[i][i];          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
           ipmx +=1;
       for(i=1;i<=nlstate;i++)          sw += weight[i];
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     } /* End theta */        } /* end of wave */
       } /* end of individual */
     trgradg =matrix(1,nlstate,1,npar);    }else if (mle==4){  /* ml=4 no 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(theta=1; theta <=npar; theta++)        for(mi=1; mi<= wav[i]-1; mi++){
         trgradg[j][theta]=gradg[theta][j];          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
     for(i=1;i<=nlstate;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       varpl[i][(int)age] =0.;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            }
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          for(d=0; d<dh[mi][i]; d++){
     for(i=1;i<=nlstate;i++)            newm=savm;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     fprintf(ficresvpl,"%.0f ",age );              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(i=1; i<=nlstate;i++)            }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          
     fprintf(ficresvpl,"\n");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     free_vector(gp,1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     free_vector(gm,1,nlstate);            savm=oldm;
     free_matrix(gradg,1,npar,1,nlstate);            oldm=newm;
     free_matrix(trgradg,1,nlstate,1,npar);          } /* end mult */
   } /* End age */        
           s1=s[mw[mi][i]][i];
   free_vector(xp,1,npar);          s2=s[mw[mi+1][i]][i];
   free_matrix(doldm,1,nlstate,1,npar);          if( s2 > nlstate){ 
   free_matrix(dnewm,1,nlstate,1,nlstate);            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
 }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }
 /************ Variance of one-step probabilities  ******************/          ipmx +=1;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)          sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int i, j;  /*      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]); */
   int k=0, cptcode;        } /* end of wave */
   double **dnewm,**doldm;      } /* end of individual */
   double *xp;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   double *gp, *gm;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double **gradg, **trgradg;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double age,agelim, cov[NCOVMAX];        for(mi=1; mi<= wav[i]-1; mi++){
   int theta;          for (ii=1;ii<=nlstate+ndeath;ii++)
   char fileresprob[FILENAMELENGTH];            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   strcpy(fileresprob,"prob");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   strcat(fileresprob,fileres);            }
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          for(d=0; d<dh[mi][i]; d++){
     printf("Problem with resultfile: %s\n", fileresprob);            newm=savm;
   }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
   xp=vector(1,npar);          
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
   cov[1]=1;            oldm=newm;
   for (age=bage; age<=fage; age ++){          } /* end mult */
     cov[2]=age;        
     gradg=matrix(1,npar,1,9);          s1=s[mw[mi][i]][i];
     trgradg=matrix(1,9,1,npar);          s2=s[mw[mi+1][i]][i];
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          ipmx +=1;
              sw += weight[i];
     for(theta=1; theta <=npar; theta++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(i=1; i<=npar; i++)          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        } /* end of wave */
            } /* end of individual */
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    } /* End of if */
        for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       k=0;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       for(i=1; i<= (nlstate+ndeath); i++){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         for(j=1; j<=(nlstate+ndeath);j++){    return -l;
            k=k+1;  }
           gp[k]=pmmij[i][j];  
         }  /*************** log-likelihood *************/
       }  double funcone( double *x)
   {
       for(i=1; i<=npar; i++)    /* Same as likeli but slower because of a lot of printf and if */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    int i, ii, j, k, mi, d, kk;
        double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     double **out;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    double lli; /* Individual log likelihood */
       k=0;    double llt;
       for(i=1; i<=(nlstate+ndeath); i++){    int s1, s2;
         for(j=1; j<=(nlstate+ndeath);j++){    double bbh, survp;
           k=k+1;    /*extern weight */
           gm[k]=pmmij[i][j];    /* We are differentiating ll according to initial status */
         }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       }    /*for(i=1;i<imx;i++) 
            printf(" %d\n",s[4][i]);
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    */
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      cov[1]=1.;
     }  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  
       for(theta=1; theta <=npar; theta++)    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       trgradg[j][theta]=gradg[theta][j];      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
        for(mi=1; mi<= wav[i]-1; mi++){
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        for (ii=1;ii<=nlstate+ndeath;ii++)
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      pmij(pmmij,cov,ncovmodel,x,nlstate);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
      k=0;        for(d=0; d<dh[mi][i]; d++){
      for(i=1; i<=(nlstate+ndeath); i++){          newm=savm;
        for(j=1; j<=(nlstate+ndeath);j++){          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
          k=k+1;          for (kk=1; kk<=cptcovage;kk++) {
          gm[k]=pmmij[i][j];            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }          }
      }          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
                out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      /*printf("\n%d ",(int)age);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
                  /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
           savm=oldm;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));          oldm=newm;
      }*/        } /* end mult */
         
   fprintf(ficresprob,"\n%d ",(int)age);        s1=s[mw[mi][i]][i];
         s2=s[mw[mi+1][i]][i];
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        bbh=(double)bh[mi][i]/(double)stepm; 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        /* bias is positive if real duration
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);         * is higher than the multiple of stepm and negative otherwise.
   }         */
         if( s2 > nlstate && (mle <5) ){  /* Jackson */
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          lli=log(out[s1][s2] - savm[s1][s2]);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        } else if  (s2==-2) {
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          for (j=1,survp=0. ; j<=nlstate; j++) 
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 }          lli= log(survp);
  free_vector(xp,1,npar);        }else if (mle==1){
 fclose(ficresprob);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
 }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         } else if(mle==3){  /* exponential inter-extrapolation */
 /******************* Printing html file ***********/          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 */
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   int jj1, k1, i1, cpt;          lli=log(out[s1][s2]); /* Original formula */
   FILE *fichtm;        } else{  /* mle=0 back to 1 */
   /*char optionfilehtm[FILENAMELENGTH];*/          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           /*lli=log(out[s1][s2]); */ /* Original formula */
   strcpy(optionfilehtm,optionfile);        } /* End of if */
   strcat(optionfilehtm,".htm");        ipmx +=1;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        sw += weight[i];
     printf("Problem with %s \n",optionfilehtm), exit(0);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         if(globpr){
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71 </font> <hr size=\"2\" color=\"#EC5E5E\">          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>   %11.6f %11.6f %11.6f ", \
                   num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
 Total number of observations=%d <br>                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
 <hr  size=\"2\" color=\"#EC5E5E\">            llt +=ll[k]*gipmx/gsw;
 <li>Outputs files<br><br>\n            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
         - 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>          fprintf(ficresilk," %10.6f\n", -llt);
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>        }
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>      } /* end of wave */
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    } /* end of individual */
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>    if(globpr==0){ /* First time we count the contributions and weights */
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>      gipmx=ipmx;
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>      gsw=sw;
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    }
      return -l;
 fprintf(fichtm," <li>Graphs</li><p>");  }
   
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
  jj1=0;  {
  for(k1=1; k1<=m;k1++){    /* This routine should help understanding what is done with 
    for(i1=1; i1<=ncodemax[k1];i1++){       the selection of individuals/waves and
        jj1++;       to check the exact contribution to the likelihood.
        if (cptcovn > 0) {       Plotting could be done.
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");     */
          for (cpt=1; cpt<=cptcoveff;cpt++)    int k;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);  
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    if(*globpri !=0){ /* Just counts and sums, no printings */
        }      strcpy(fileresilk,"ilk"); 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      strcat(fileresilk,fileres);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          if((ficresilk=fopen(fileresilk,"w"))==NULL) {
        for(cpt=1; cpt<nlstate;cpt++){        printf("Problem with resultfile: %s\n", fileresilk);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      }
        }      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");
     for(cpt=1; cpt<=nlstate;cpt++) {      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
 interval) in state (%d): v%s%d%d.gif <br>      for(k=1; k<=nlstate; k++) 
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
      }      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
      for(cpt=1; cpt<=nlstate;cpt++) {    }
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>  
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    *fretone=(*funcone)(p);
      }    if(*globpri !=0){
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      fclose(ficresilk);
 health expectancies in states (1) and (2): e%s%d.gif<br>      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      fflush(fichtm); 
 fprintf(fichtm,"\n</body>");    } 
    }    return;
    }  }
 fclose(fichtm);  
 }  
   /*********** Maximum Likelihood Estimation ***************/
 /******************* Gnuplot file **************/  
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    int i,j, iter;
     double **xi;
   strcpy(optionfilegnuplot,optionfilefiname);    double fret;
   strcat(optionfilegnuplot,".plt");    double fretone; /* Only one call to likelihood */
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    /*  char filerespow[FILENAMELENGTH];*/
     printf("Problem with file %s",optionfilegnuplot);    xi=matrix(1,npar,1,npar);
   }    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
 #ifdef windows        xi[i][j]=(i==j ? 1.0 : 0.0);
     fprintf(ficgp,"cd \"%s\" \n",pathc);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
 #endif    strcpy(filerespow,"pow"); 
 m=pow(2,cptcoveff);    strcat(filerespow,fileres);
      if((ficrespow=fopen(filerespow,"w"))==NULL) {
  /* 1eme*/      printf("Problem with resultfile: %s\n", filerespow);
   for (cpt=1; cpt<= nlstate ; cpt ++) {      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
    for (k1=1; k1<= m ; k1 ++) {    }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
 #ifdef windows    for (i=1;i<=nlstate;i++)
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);      for(j=1;j<=nlstate+ndeath;j++)
 #endif        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
 #ifdef unix    fprintf(ficrespow,"\n");
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);  
 #endif    powell(p,xi,npar,ftol,&iter,&fret,func);
   
 for (i=1; i<= nlstate ; i ++) {    free_matrix(xi,1,npar,1,npar);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    fclose(ficrespow);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    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(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }  /**** Computes Hessian and covariance matrix ***/
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
      for (i=1; i<= nlstate ; i ++) {  {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    double  **a,**y,*x,pd;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double **hess;
 }      int i, j,jk;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    int *indx;
 #ifdef unix  
 fprintf(ficgp,"\nset ter gif small size 400,300");    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
 #endif    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    void lubksb(double **a, int npar, int *indx, double b[]) ;
    }    void ludcmp(double **a, int npar, int *indx, double *d) ;
   }    double gompertz(double p[]);
   /*2 eme*/    hess=matrix(1,npar,1,npar);
   
   for (k1=1; k1<= m ; k1 ++) {    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
        for (i=1;i<=npar;i++){
     for (i=1; i<= nlstate+1 ; i ++) {      printf("%d",i);fflush(stdout);
       k=2*i;      fprintf(ficlog,"%d",i);fflush(ficlog);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);     
       for (j=1; j<= nlstate+1 ; j ++) {       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      
   else fprintf(ficgp," \%%*lf (\%%*lf)");      /*  printf(" %f ",p[i]);
 }            printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    for (i=1;i<=npar;i++) {
       for (j=1; j<= nlstate+1 ; j ++) {      for (j=1;j<=npar;j++)  {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        if (j>i) { 
         else fprintf(ficgp," \%%*lf (\%%*lf)");          printf(".%d%d",i,j);fflush(stdout);
 }            fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
       fprintf(ficgp,"\" t\"\" w l 0,");          hess[i][j]=hessij(p,delti,i,j,func,npar);
      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 ++) {          hess[j][i]=hess[i][j];    
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          /*printf(" %lf ",hess[i][j]);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }        }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    }
       else fprintf(ficgp,"\" t\"\" w l 0,");    printf("\n");
     }    fprintf(ficlog,"\n");
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);  
   }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
      fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   /*3eme*/    
     a=matrix(1,npar,1,npar);
   for (k1=1; k1<= m ; k1 ++) {    y=matrix(1,npar,1,npar);
     for (cpt=1; cpt<= nlstate ; cpt ++) {    x=vector(1,npar);
       k=2+nlstate*(cpt-1);    indx=ivector(1,npar);
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);    for (i=1;i<=npar;i++)
       for (i=1; i< nlstate ; i ++) {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         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);    ludcmp(a,npar,indx,&pd);
       }  
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    for (j=1;j<=npar;j++) {
     }      for (i=1;i<=npar;i++) x[i]=0;
     }      x[j]=1;
        lubksb(a,npar,indx,x);
   /* CV preval stat */      for (i=1;i<=npar;i++){ 
     for (k1=1; k1<= m ; k1 ++) {        matcov[i][j]=x[i];
     for (cpt=1; cpt<nlstate ; cpt ++) {      }
       k=3;    }
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);  
     printf("\n#Hessian matrix#\n");
       for (i=1; i< nlstate ; i ++)    fprintf(ficlog,"\n#Hessian matrix#\n");
         fprintf(ficgp,"+$%d",k+i+1);    for (i=1;i<=npar;i++) { 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      for (j=1;j<=npar;j++) { 
              printf("%.3e ",hess[i][j]);
       l=3+(nlstate+ndeath)*cpt;        fprintf(ficlog,"%.3e ",hess[i][j]);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      }
       for (i=1; i< nlstate ; i ++) {      printf("\n");
         l=3+(nlstate+ndeath)*cpt;      fprintf(ficlog,"\n");
         fprintf(ficgp,"+$%d",l+i+1);    }
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      /* Recompute Inverse */
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    for (i=1;i<=npar;i++)
     }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   }      ludcmp(a,npar,indx,&pd);
    
   /* proba elementaires */    /*  printf("\n#Hessian matrix recomputed#\n");
    for(i=1,jk=1; i <=nlstate; i++){  
     for(k=1; k <=(nlstate+ndeath); k++){    for (j=1;j<=npar;j++) {
       if (k != i) {      for (i=1;i<=npar;i++) x[i]=0;
         for(j=1; j <=ncovmodel; j++){      x[j]=1;
              lubksb(a,npar,indx,x);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      for (i=1;i<=npar;i++){ 
           jk++;        y[i][j]=x[i];
           fprintf(ficgp,"\n");        printf("%.3e ",y[i][j]);
         }        fprintf(ficlog,"%.3e ",y[i][j]);
       }      }
     }      printf("\n");
     }      fprintf(ficlog,"\n");
     }
     for(jk=1; jk <=m; jk++) {    */
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);  
    i=1;    free_matrix(a,1,npar,1,npar);
    for(k2=1; k2<=nlstate; k2++) {    free_matrix(y,1,npar,1,npar);
      k3=i;    free_vector(x,1,npar);
      for(k=1; k<=(nlstate+ndeath); k++) {    free_ivector(indx,1,npar);
        if (k != k2){    free_matrix(hess,1,npar,1,npar);
         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]]]);  /*************** hessian matrix ****************/
             ij++;  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
           }  {
           else    int i;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    int l=1, lmax=20;
         }    double k1,k2;
           fprintf(ficgp,")/(1");    double p2[MAXPARM+1]; /* identical to x */
            double res;
         for(k1=1; k1 <=nlstate; k1++){      double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    double fx;
 ij=1;    int k=0,kmax=10;
           for(j=3; j <=ncovmodel; j++){    double l1;
           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]]]);    fx=func(x);
             ij++;    for (i=1;i<=npar;i++) p2[i]=x[i];
           }    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
           else      l1=pow(10,l);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      delts=delt;
           }      for(k=1 ; k <kmax; k=k+1){
           fprintf(ficgp,")");        delt = delta*(l1*k);
         }        p2[theta]=x[theta] +delt;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        p2[theta]=x[theta]-delt;
         i=i+ncovmodel;        k2=func(p2)-fx;
        }        /*res= (k1-2.0*fx+k2)/delt/delt; */
      }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
    }        
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  #ifdef DEBUGHESS
    }        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
            fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   fclose(ficgp);  #endif
 }  /* end gnuplot */        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
 /*************** Moving average **************/        }
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10.;
   int i, cpt, cptcod;        }
     for (agedeb=agemin; agedeb<=fage; agedeb++)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       for (i=1; i<=nlstate;i++)          delts=delt;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        }
           mobaverage[(int)agedeb][i][cptcod]=0.;      }
        }
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){    delti[theta]=delts;
       for (i=1; i<=nlstate;i++){    return res; 
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    
           for (cpt=0;cpt<=4;cpt++){  }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];  
           }  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  {
         }    int i;
       }    int l=1, l1, lmax=20;
     }    double k1,k2,k3,k4,res,fx;
        double p2[MAXPARM+1];
 }    int k;
   
     fx=func(x);
 /************** Forecasting ******************/    for (k=1; k<=2; k++) {
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){      for (i=1;i<=npar;i++) p2[i]=x[i];
        p2[thetai]=x[thetai]+delti[thetai]/k;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   int *popage;      k1=func(p2)-fx;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    
   double *popeffectif,*popcount;      p2[thetai]=x[thetai]+delti[thetai]/k;
   double ***p3mat;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   char fileresf[FILENAMELENGTH];      k2=func(p2)-fx;
     
  agelim=AGESUP;      p2[thetai]=x[thetai]-delti[thetai]/k;
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    
        p2[thetai]=x[thetai]-delti[thetai]/k;
        p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   strcpy(fileresf,"f");      k4=func(p2)-fx;
   strcat(fileresf,fileres);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   if((ficresf=fopen(fileresf,"w"))==NULL) {  #ifdef DEBUG
     printf("Problem with forecast resultfile: %s\n", fileresf);      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   }      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   printf("Computing forecasting: result on file '%s' \n", fileresf);  #endif
     }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    return res;
   }
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /************** Inverse of matrix **************/
     movingaverage(agedeb, fage, agemin, mobaverage);  void ludcmp(double **a, int n, int *indx, double *d) 
   }  { 
     int i,imax,j,k; 
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double big,dum,sum,temp; 
   if (stepm<=12) stepsize=1;    double *vv; 
     
   agelim=AGESUP;    vv=vector(1,n); 
      *d=1.0; 
   hstepm=1;    for (i=1;i<=n;i++) { 
   hstepm=hstepm/stepm;      big=0.0; 
   yp1=modf(dateintmean,&yp);      for (j=1;j<=n;j++) 
   anprojmean=yp;        if ((temp=fabs(a[i][j])) > big) big=temp; 
   yp2=modf((yp1*12),&yp);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   mprojmean=yp;      vv[i]=1.0/big; 
   yp1=modf((yp2*30.5),&yp);    } 
   jprojmean=yp;    for (j=1;j<=n;j++) { 
   if(jprojmean==0) jprojmean=1;      for (i=1;i<j;i++) { 
   if(mprojmean==0) jprojmean=1;        sum=a[i][j]; 
          for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        a[i][j]=sum; 
        } 
   for(cptcov=1;cptcov<=i2;cptcov++){      big=0.0; 
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for (i=j;i<=n;i++) { 
       k=k+1;        sum=a[i][j]; 
       fprintf(ficresf,"\n#******");        for (k=1;k<j;k++) 
       for(j=1;j<=cptcoveff;j++) {          sum -= a[i][k]*a[k][j]; 
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        a[i][j]=sum; 
       }        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       fprintf(ficresf,"******\n");          big=dum; 
       fprintf(ficresf,"# StartingAge FinalAge");          imax=i; 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        } 
            } 
            if (j != imax) { 
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {        for (k=1;k<=n;k++) { 
         fprintf(ficresf,"\n");          dum=a[imax][k]; 
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){        } 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        *d = -(*d); 
           nhstepm = nhstepm/hstepm;        vv[imax]=vv[j]; 
                } 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      indx[j]=imax; 
           oldm=oldms;savm=savms;      if (a[j][j] == 0.0) a[j][j]=TINY; 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        if (j != n) { 
                dum=1.0/(a[j][j]); 
           for (h=0; h<=nhstepm; h++){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
             if (h==(int) (calagedate+YEARM*cpt)) {      } 
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);    } 
             }    free_vector(vv,1,n);  /* Doesn't work */
             for(j=1; j<=nlstate+ndeath;j++) {  ;
               kk1=0.;kk2=0;  } 
               for(i=1; i<=nlstate;i++) {                
                 if (mobilav==1)  void lubksb(double **a, int n, int *indx, double b[]) 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  { 
                 else {    int i,ii=0,ip,j; 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    double sum; 
                 }   
                    for (i=1;i<=n;i++) { 
               }      ip=indx[i]; 
               if (h==(int)(calagedate+12*cpt)){      sum=b[ip]; 
                 fprintf(ficresf," %.3f", kk1);      b[ip]=b[i]; 
                              if (ii) 
               }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
             }      else if (sum) ii=i; 
           }      b[i]=sum; 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    } 
         }    for (i=n;i>=1;i--) { 
       }      sum=b[i]; 
     }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   }      b[i]=sum/a[i][i]; 
            } 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  } 
   
   fclose(ficresf);  void pstamp(FILE *fichier)
 }  {
 /************** Forecasting ******************/    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){  }
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  /************ Frequencies ********************/
   int *popage;  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[])
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  {  /* Some frequencies */
   double *popeffectif,*popcount;    
   double ***p3mat,***tabpop,***tabpopprev;    int i, m, jk, k1,i1, j1, bool, z1,j;
   char filerespop[FILENAMELENGTH];    int first;
     double ***freq; /* Frequencies */
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double *pp, **prop;
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   agelim=AGESUP;    char fileresp[FILENAMELENGTH];
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    
      pp=vector(1,nlstate);
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    prop=matrix(1,nlstate,iagemin,iagemax+3);
      strcpy(fileresp,"p");
      strcat(fileresp,fileres);
   strcpy(filerespop,"pop");    if((ficresp=fopen(fileresp,"w"))==NULL) {
   strcat(filerespop,fileres);      printf("Problem with prevalence resultfile: %s\n", fileresp);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     printf("Problem with forecast resultfile: %s\n", filerespop);      exit(0);
   }    }
   printf("Computing forecasting: result on file '%s' \n", filerespop);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    
     j=cptcoveff;
   if (mobilav==1) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     movingaverage(agedeb, fage, agemin, mobaverage);    first=1;
   }  
     /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
   if (stepm<=12) stepsize=1;    /*    j1++;
    */
   agelim=AGESUP;    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
          /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   hstepm=1;          scanf("%d", i);*/
   hstepm=hstepm/stepm;        for (i=-5; i<=nlstate+ndeath; i++)  
            for (jk=-5; jk<=nlstate+ndeath; jk++)  
   if (popforecast==1) {            for(m=iagemin; m <= iagemax+3; m++)
     if((ficpop=fopen(popfile,"r"))==NULL) {              freq[i][jk][m]=0;
       printf("Problem with population file : %s\n",popfile);exit(0);        
     }        for (i=1; i<=nlstate; i++)  
     popage=ivector(0,AGESUP);          for(m=iagemin; m <= iagemax+3; m++)
     popeffectif=vector(0,AGESUP);            prop[i][m]=0;
     popcount=vector(0,AGESUP);        
            dateintsum=0;
     i=1;          k2cpt=0;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        for (i=1; i<=imx; i++) {
              bool=1;
     imx=i;          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];            for (z1=1; z1<=cptcoveff; z1++)       
   }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
                   /* Tests if the value of each of the covariates of i is equal to filter j1 */
   for(cptcov=1;cptcov<=i2;cptcov++){                bool=0;
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n", 
       k=k+1;                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
       fprintf(ficrespop,"\n#******");                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
       for(j=1;j<=cptcoveff;j++) {                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              } 
       }          }
       fprintf(ficrespop,"******\n");   
       fprintf(ficrespop,"# Age");          if (bool==1){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);            for(m=firstpass; m<=lastpass; m++){
       if (popforecast==1)  fprintf(ficrespop," [Population]");              k2=anint[m][i]+(mint[m][i]/12.);
                    /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       for (cpt=0; cpt<=0;cpt++) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                  if(agev[m][i]==1) agev[m][i]=iagemax+2;
                        if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){                if (m<lastpass) {
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           nhstepm = nhstepm/hstepm;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                          }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                
           oldm=oldms;savm=savms;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                    dateintsum=dateintsum+k2;
                          k2cpt++;
           for (h=0; h<=nhstepm; h++){                }
             if (h==(int) (calagedate+YEARM*cpt)) {                /*}*/
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            }
             }          }
             for(j=1; j<=nlstate+ndeath;j++) {        } /* end i */
               kk1=0.;kk2=0;         
               for(i=1; i<=nlstate;i++) {                      /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
                 if (mobilav==1)        pstamp(ficresp);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        if  (cptcovn>0) {
                 else {          fprintf(ficresp, "\n#********** Variable "); 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                 }          fprintf(ficresp, "**********\n#");
               }          fprintf(ficlog, "\n#********** Variable "); 
               if (h==(int)(calagedate+12*cpt)){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          fprintf(ficlog, "**********\n#");
                   /*fprintf(ficrespop," %.3f", kk1);        }
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        for(i=1; i<=nlstate;i++) 
               }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
             }        fprintf(ficresp, "\n");
             for(i=1; i<=nlstate;i++){        
               kk1=0.;        for(i=iagemin; i <= iagemax+3; i++){
                 for(j=1; j<=nlstate;j++){          if(i==iagemax+3){
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];            fprintf(ficlog,"Total");
                 }          }else{
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];            if(first==1){
             }              first=0;
               printf("See log file for details...\n");
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)            }
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);            fprintf(ficlog,"Age %d", i);
           }          }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(jk=1; jk <=nlstate ; jk++){
         }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       }              pp[jk] += freq[jk][m][i]; 
            }
   /******/          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {              pos += freq[jk][m][i];
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);              if(pp[jk]>=1.e-10){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){              if(first==1){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           nhstepm = nhstepm/hstepm;              }
                        fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }else{
           oldm=oldms;savm=savms;              if(first==1)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                  printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           for (h=0; h<=nhstepm; h++){              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             if (h==(int) (calagedate+YEARM*cpt)) {            }
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          }
             }  
             for(j=1; j<=nlstate+ndeath;j++) {          for(jk=1; jk <=nlstate ; jk++){
               kk1=0.;kk2=0;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               for(i=1; i<=nlstate;i++) {                            pp[jk] += freq[jk][m][i];
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              }       
               }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);            pos += pp[jk];
             }            posprop += prop[jk][i];
           }          }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(jk=1; jk <=nlstate ; jk++){
         }            if(pos>=1.e-5){
       }              if(first==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 (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   if (popforecast==1) {              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     free_ivector(popage,0,AGESUP);            }
     free_vector(popeffectif,0,AGESUP);            if( i <= iagemax){
     free_vector(popcount,0,AGESUP);              if(pos>=1.e-5){
   }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                /*probs[i][jk][j1]= pp[jk]/pos;*/
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   fclose(ficrespop);              }
 }              else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
 /***********************************************/            }
 /**************** Main Program *****************/          }
 /***********************************************/          
           for(jk=-1; jk <=nlstate+ndeath; jk++)
 int main(int argc, char *argv[])            for(m=-1; m <=nlstate+ndeath; m++)
 {              if(freq[jk][m][i] !=0 ) {
               if(first==1)
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   double agedeb, agefin,hf;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;              }
           if(i <= iagemax)
   double fret;            fprintf(ficresp,"\n");
   double **xi,tmp,delta;          if(first==1)
             printf("Others in log...\n");
   double dum; /* Dummy variable */          fprintf(ficlog,"\n");
   double ***p3mat;        }
   int *indx;        /*}*/
   char line[MAXLINE], linepar[MAXLINE];    }
   char title[MAXLINE];    dateintmean=dateintsum/k2cpt; 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];   
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    fclose(ficresp);
      free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   char filerest[FILENAMELENGTH];    /* End of Freq */
   char fileregp[FILENAMELENGTH];  }
   char popfile[FILENAMELENGTH];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  /************ Prevalence ********************/
   int firstobs=1, lastobs=10;  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)
   int sdeb, sfin; /* Status at beginning and end */  {  
   int c,  h , cpt,l;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   int ju,jl, mi;       in each health status at the date of interview (if between dateprev1 and dateprev2).
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;       We still use firstpass and lastpass as another selection.
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    */
   int mobilav=0,popforecast=0;   
   int hstepm, nhstepm;    int i, m, jk, k1, i1, j1, bool, z1,j;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    double ***freq; /* Frequencies */
     double *pp, **prop;
   double bage, fage, age, agelim, agebase;    double pos,posprop; 
   double ftolpl=FTOL;    double  y2; /* in fractional years */
   double **prlim;    int iagemin, iagemax;
   double *severity;    int first; /** to stop verbosity which is redirected to log file */
   double ***param; /* Matrix of parameters */  
   double  *p;    iagemin= (int) agemin;
   double **matcov; /* Matrix of covariance */    iagemax= (int) agemax;
   double ***delti3; /* Scale */    /*pp=vector(1,nlstate);*/
   double *delti; /* Scale */    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   double ***eij, ***vareij;    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   double **varpl; /* Variances of prevalence limits by age */    j1=0;
   double *epj, vepp;    
   double kk1, kk2;    /*j=cptcoveff;*/
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      
     first=1;
   char version[80]="Imach version 0.71, February 2002, INED-EUROREVES ";    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
   char *alph[]={"a","a","b","c","d","e"}, str[4];      /*for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;*/
         
   char z[1]="c", occ;        for (i=1; i<=nlstate; i++)  
 #include <sys/time.h>          for(m=iagemin; m <= iagemax+3; m++)
 #include <time.h>            prop[i][m]=0.0;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];       
          for (i=1; i<=imx; i++) { /* Each individual */
   /* long total_usecs;          bool=1;
   struct timeval start_time, end_time;          if  (cptcovn>0) {
              for (z1=1; z1<=cptcoveff; z1++) 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
           } 
   printf("\n%s",version);          if (bool==1) { 
   if(argc <=1){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     printf("\nEnter the parameter file name: ");              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     scanf("%s",pathtot);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   else{                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     strcpy(pathtot,argv[1]);                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   }                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/                  /*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]]);*/
   /*cygwin_split_path(pathtot,path,optionfile);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/                  prop[s[m][i]][iagemax+3] += weight[i]; 
   /* cutv(path,optionfile,pathtot,'\\');*/                } 
               }
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);            } /* end selection of waves */
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);          }
   chdir(path);        }
   replace(pathc,path);        for(i=iagemin; i <= iagemax+3; i++){  
           for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
 /*-------- arguments in the command line --------*/            posprop += prop[jk][i]; 
           } 
   strcpy(fileres,"r");          
   strcat(fileres, optionfilefiname);          for(jk=1; jk <=nlstate ; jk++){     
   strcat(fileres,".txt");    /* Other files have txt extension */            if( i <=  iagemax){ 
               if(posprop>=1.e-5){ 
   /*---------arguments file --------*/                probs[i][jk][j1]= prop[jk][i]/posprop;
               } else{
   if((ficpar=fopen(optionfile,"r"))==NULL)    {                if(first==1){
     printf("Problem with optionfile %s\n",optionfile);                  first=0;
     goto end;                  printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
   }                }
               }
   strcpy(filereso,"o");            } 
   strcat(filereso,fileres);          }/* end jk */ 
   if((ficparo=fopen(filereso,"w"))==NULL) {        }/* end i */ 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      /*} *//* end i1 */
   }    } /* end j1 */
     
   /* Reads comments: lines beginning with '#' */    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   while((c=getc(ficpar))=='#' && c!= EOF){    /*free_vector(pp,1,nlstate);*/
     ungetc(c,ficpar);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     fgets(line, MAXLINE, ficpar);  }  /* End of prevalence */
     puts(line);  
     fputs(line,ficparo);  /************* Waves Concatenation ***************/
   }  
   ungetc(c,ficpar);  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)
   {
   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);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   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);       Death is a valid wave (if date is known).
   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);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
 while((c=getc(ficpar))=='#' && c!= EOF){       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     ungetc(c,ficpar);       and mw[mi+1][i]. dh depends on stepm.
     fgets(line, MAXLINE, ficpar);       */
     puts(line);  
     fputs(line,ficparo);    int i, mi, m;
   }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   ungetc(c,ficpar);       double sum=0., jmean=0.;*/
      int first;
        int j, k=0,jk, ju, jl;
   covar=matrix(0,NCOVMAX,1,n);    double sum=0.;
   cptcovn=0;    first=0;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    jmin=1e+5;
     jmax=-1;
   ncovmodel=2+cptcovn;    jmean=0.;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    for(i=1; i<=imx; i++){
        mi=0;
   /* Read guess parameters */      m=firstpass;
   /* Reads comments: lines beginning with '#' */      while(s[m][i] <= nlstate){
   while((c=getc(ficpar))=='#' && c!= EOF){        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
     ungetc(c,ficpar);          mw[++mi][i]=m;
     fgets(line, MAXLINE, ficpar);        if(m >=lastpass)
     puts(line);          break;
     fputs(line,ficparo);        else
   }          m++;
   ungetc(c,ficpar);      }/* end while */
        if (s[m][i] > nlstate){
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        mi++;     /* Death is another wave */
     for(i=1; i <=nlstate; i++)        /* if(mi==0)  never been interviewed correctly before death */
     for(j=1; j <=nlstate+ndeath-1; j++){           /* Only death is a correct wave */
       fscanf(ficpar,"%1d%1d",&i1,&j1);        mw[mi][i]=m;
       fprintf(ficparo,"%1d%1d",i1,j1);      }
       printf("%1d%1d",i,j);  
       for(k=1; k<=ncovmodel;k++){      wav[i]=mi;
         fscanf(ficpar," %lf",&param[i][j][k]);      if(mi==0){
         printf(" %lf",param[i][j][k]);        nbwarn++;
         fprintf(ficparo," %lf",param[i][j][k]);        if(first==0){
       }          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       fscanf(ficpar,"\n");          first=1;
       printf("\n");        }
       fprintf(ficparo,"\n");        if(first==1){
     }          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
          }
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      } /* end mi==0 */
     } /* End individuals */
   p=param[1][1];  
      for(i=1; i<=imx; i++){
   /* Reads comments: lines beginning with '#' */      for(mi=1; mi<wav[i];mi++){
   while((c=getc(ficpar))=='#' && c!= EOF){        if (stepm <=0)
     ungetc(c,ficpar);          dh[mi][i]=1;
     fgets(line, MAXLINE, ficpar);        else{
     puts(line);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     fputs(line,ficparo);            if (agedc[i] < 2*AGESUP) {
   }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   ungetc(c,ficpar);              if(j==0) j=1;  /* Survives at least one month after exam */
               else if(j<0){
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                nberr++;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */                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]);
   for(i=1; i <=nlstate; i++){                j=1; /* Temporary Dangerous patch */
     for(j=1; j <=nlstate+ndeath-1; j++){                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);
       fscanf(ficpar,"%1d%1d",&i1,&j1);                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]);
       printf("%1d%1d",i,j);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
       fprintf(ficparo,"%1d%1d",i1,j1);              }
       for(k=1; k<=ncovmodel;k++){              k=k+1;
         fscanf(ficpar,"%le",&delti3[i][j][k]);              if (j >= jmax){
         printf(" %le",delti3[i][j][k]);                jmax=j;
         fprintf(ficparo," %le",delti3[i][j][k]);                ijmax=i;
       }              }
       fscanf(ficpar,"\n");              if (j <= jmin){
       printf("\n");                jmin=j;
       fprintf(ficparo,"\n");                ijmin=i;
     }              }
   }              sum=sum+j;
   delti=delti3[1][1];              /*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);*/
   /* Reads comments: lines beginning with '#' */            }
   while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);          else{
     fgets(line, MAXLINE, ficpar);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     puts(line);  /*        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]); */
     fputs(line,ficparo);  
   }            k=k+1;
   ungetc(c,ficpar);            if (j >= jmax) {
                jmax=j;
   matcov=matrix(1,npar,1,npar);              ijmax=i;
   for(i=1; i <=npar; i++){            }
     fscanf(ficpar,"%s",&str);            else if (j <= jmin){
     printf("%s",str);              jmin=j;
     fprintf(ficparo,"%s",str);              ijmin=i;
     for(j=1; j <=i; j++){            }
       fscanf(ficpar," %le",&matcov[i][j]);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       printf(" %.5le",matcov[i][j]);            /*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]);*/
       fprintf(ficparo," %.5le",matcov[i][j]);            if(j<0){
     }              nberr++;
     fscanf(ficpar,"\n");              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]);
     printf("\n");              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]);
     fprintf(ficparo,"\n");            }
   }            sum=sum+j;
   for(i=1; i <=npar; i++)          }
     for(j=i+1;j<=npar;j++)          jk= j/stepm;
       matcov[i][j]=matcov[j][i];          jl= j -jk*stepm;
              ju= j -(jk+1)*stepm;
   printf("\n");          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             if(jl==0){
               dh[mi][i]=jk;
     /*-------- Rewriting paramater file ----------*/              bh[mi][i]=0;
      strcpy(rfileres,"r");    /* "Rparameterfile */            }else{ /* We want a negative bias in order to only have interpolation ie
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/                    * to avoid the price of an extra matrix product in likelihood */
      strcat(rfileres,".");    /* */              dh[mi][i]=jk+1;
      strcat(rfileres,optionfilext);    /* Other files have txt extension */              bh[mi][i]=ju;
     if((ficres =fopen(rfileres,"w"))==NULL) {            }
       printf("Problem writing new parameter file: %s\n", fileres);goto end;          }else{
     }            if(jl <= -ju){
     fprintf(ficres,"#%s\n",version);              dh[mi][i]=jk;
                  bh[mi][i]=jl;       /* bias is positive if real duration
     /*-------- data file ----------*/                                   * is higher than the multiple of stepm and negative otherwise.
     if((fic=fopen(datafile,"r"))==NULL)    {                                   */
       printf("Problem with datafile: %s\n", datafile);goto end;            }
     }            else{
               dh[mi][i]=jk+1;
     n= lastobs;              bh[mi][i]=ju;
     severity = vector(1,maxwav);            }
     outcome=imatrix(1,maxwav+1,1,n);            if(dh[mi][i]==0){
     num=ivector(1,n);              dh[mi][i]=1; /* At least one step */
     moisnais=vector(1,n);              bh[mi][i]=ju; /* At least one step */
     annais=vector(1,n);              /*  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);*/
     moisdc=vector(1,n);            }
     andc=vector(1,n);          } /* end if mle */
     agedc=vector(1,n);        }
     cod=ivector(1,n);      } /* end wave */
     weight=vector(1,n);    }
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    jmean=sum/k;
     mint=matrix(1,maxwav,1,n);    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);
     anint=matrix(1,maxwav,1,n);    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
     s=imatrix(1,maxwav+1,1,n);   }
     adl=imatrix(1,maxwav+1,1,n);      
     tab=ivector(1,NCOVMAX);  /*********** Tricode ****************************/
     ncodemax=ivector(1,8);  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   {
     i=1;    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
     while (fgets(line, MAXLINE, fic) != NULL)    {    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
       if ((i >= firstobs) && (i <=lastobs)) {    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
             * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
         for (j=maxwav;j>=1;j--){    /* nbcode[Tvar[j]][1]= 
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    */
           strcpy(line,stra);  
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    int modmaxcovj=0; /* Modality max of covariates j */
         }    int cptcode=0; /* Modality max of covariates j */
            int modmincovj=0; /* Modality min of covariates j */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  
     cptcoveff=0; 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);   
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    for (k=-1; k < maxncov; k++) Ndum[k]=0;
     for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  
         for (j=ncov;j>=1;j--){    /* Loop on covariates without age and products */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
         }      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
         num[i]=atol(stra);                                 modality of this covariate Vj*/ 
                ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){                                      * If product of Vn*Vm, still boolean *:
           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;}*/                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
                                       * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
         i=i+1;        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
       }                                        modality of the nth covariate of individual i. */
     }        if (ij > modmaxcovj)
     /* printf("ii=%d", ij);          modmaxcovj=ij; 
        scanf("%d",i);*/        else if (ij < modmincovj) 
   imx=i-1; /* Number of individuals */          modmincovj=ij; 
         if ((ij < -1) && (ij > NCOVMAX)){
   /* for (i=1; i<=imx; i++){          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          exit(1);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;        }else
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
     }        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     for (i=1; i<=imx; i++)        /* getting the maximum value of the modality of the covariate
     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]));*/           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
            female is 1, then modmaxcovj=1.*/
   /* Calculation of the number of parameter from char model*/      }
   Tvar=ivector(1,15);      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
   Tprod=ivector(1,15);      cptcode=modmaxcovj;
   Tvaraff=ivector(1,15);      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
   Tvard=imatrix(1,15,1,2);     /*for (i=0; i<=cptcode; i++) {*/
   Tage=ivector(1,15);            for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
            printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
   if (strlen(model) >1){        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
     j=0, j1=0, k1=1, k2=1;          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
     j=nbocc(model,'+');        }
     j1=nbocc(model,'*');        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
     cptcovn=j+1;           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
     cptcovprod=j1;      } /* Ndum[-1] number of undefined modalities */
      
          /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
     strcpy(modelsav,model);      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
       printf("Error. Non available option model=%s ",model);         modmincovj=3; modmaxcovj = 7;
       goto end;         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
     }         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
             variables V1_1 and V1_2.
     for(i=(j+1); i>=1;i--){         nbcode[Tvar[j]][ij]=k;
       cutv(stra,strb,modelsav,'+');         nbcode[Tvar[j]][1]=0;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);         nbcode[Tvar[j]][2]=1;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/         nbcode[Tvar[j]][3]=2;
       /*scanf("%d",i);*/      */
       if (strchr(strb,'*')) {      ij=1; /* ij is similar to i but can jumps over null modalities */
         cutv(strd,strc,strb,'*');      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
         if (strcmp(strc,"age")==0) {        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
           cptcovprod--;          /*recode from 0 */
           cutv(strb,stre,strd,'V');          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
           Tvar[i]=atoi(stre);            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
           cptcovage++;                                       k is a modality. If we have model=V1+V1*sex 
             Tage[cptcovage]=i;                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
             /*printf("stre=%s ", stre);*/            ij++;
         }          }
         else if (strcmp(strd,"age")==0) {          if (ij > ncodemax[j]) break; 
           cptcovprod--;        }  /* end of loop on */
           cutv(strb,stre,strc,'V');      } /* end of loop on modality */ 
           Tvar[i]=atoi(stre);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
           cptcovage++;    
           Tage[cptcovage]=i;   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
         }    
         else {    for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
           cutv(strb,stre,strc,'V');     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
           Tvar[i]=ncov+k1;     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
           cutv(strb,strc,strd,'V');     Ndum[ij]++; 
           Tprod[k1]=i;   } 
           Tvard[k1][1]=atoi(strc);  
           Tvard[k1][2]=atoi(stre);   ij=1;
           Tvar[cptcovn+k2]=Tvard[k1][1];   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
           for (k=1; k<=lastobs;k++)     if((Ndum[i]!=0) && (i<=ncovcol)){
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
           k1++;       Tvaraff[ij]=i; /*For printing (unclear) */
           k2=k2+2;       ij++;
         }     }else
       }         Tvaraff[ij]=0;
       else {   }
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/   ij--;
        /*  scanf("%d",i);*/   cptcoveff=ij; /*Number of total covariates*/
       cutv(strd,strc,strb,'V');  
       Tvar[i]=atoi(strc);  }
       }  
       strcpy(modelsav,stra);    
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  /*********** Health Expectancies ****************/
         scanf("%d",i);*/  
     }  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
 }  
    {
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    /* Health expectancies, no variances */
   printf("cptcovprod=%d ", cptcovprod);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   scanf("%d ",i);*/    int nhstepma, nstepma; /* Decreasing with age */
     fclose(fic);    double age, agelim, hf;
     double ***p3mat;
     /*  if(mle==1){*/    double eip;
     if (weightopt != 1) { /* Maximisation without weights*/  
       for(i=1;i<=n;i++) weight[i]=1.0;    pstamp(ficreseij);
     }    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     /*-calculation of age at interview from date of interview and age at death -*/    fprintf(ficreseij,"# Age");
     agev=matrix(1,maxwav,1,imx);    for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++){
    for (i=1; i<=imx; i++)        fprintf(ficreseij," e%1d%1d ",i,j);
      for(m=2; (m<= maxwav); m++)      }
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      fprintf(ficreseij," e%1d. ",i);
          anint[m][i]=9999;    }
          s[m][i]=-1;    fprintf(ficreseij,"\n");
        }  
        
     for (i=1; i<=imx; i++)  {    if(estepm < stepm){
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      printf ("Problem %d lower than %d\n",estepm, stepm);
       for(m=1; (m<= maxwav); m++){    }
         if(s[m][i] >0){    else  hstepm=estepm;   
           if (s[m][i] == nlstate+1) {    /* We compute the life expectancy from trapezoids spaced every estepm months
             if(agedc[i]>0)     * This is mainly to measure the difference between two models: for example
               if(moisdc[i]!=99 && andc[i]!=9999)     * if stepm=24 months pijx are given only every 2 years and by summing them
               agev[m][i]=agedc[i];     * we are calculating an estimate of the Life Expectancy assuming a linear 
             else {     * progression in between and thus overestimating or underestimating according
               if (andc[i]!=9999){     * to the curvature of the survival function. If, for the same date, we 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
               agev[m][i]=-1;     * to compare the new estimate of Life expectancy with the same linear 
               }     * hypothesis. A more precise result, taking into account a more precise
             }     * curvature will be obtained if estepm is as small as stepm. */
           }  
           else if(s[m][i] !=9){ /* Should no more exist */    /* For example we decided to compute the life expectancy with the smallest unit */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
             if(mint[m][i]==99 || anint[m][i]==9999)       nhstepm is the number of hstepm from age to agelim 
               agev[m][i]=1;       nstepm is the number of stepm from age to agelin. 
             else if(agev[m][i] <agemin){       Look at hpijx to understand the reason of that which relies in memory size
               agemin=agev[m][i];       and note for a fixed period like estepm months */
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
             }       survival function given by stepm (the optimization length). Unfortunately it
             else if(agev[m][i] >agemax){       means that if the survival funtion is printed only each two years of age and if
               agemax=agev[m][i];       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/       results. So we changed our mind and took the option of the best precision.
             }    */
             /*agev[m][i]=anint[m][i]-annais[i];*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
             /*   agev[m][i] = age[i]+2*m;*/  
           }    agelim=AGESUP;
           else { /* =9 */    /* If stepm=6 months */
             agev[m][i]=1;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
             s[m][i]=-1;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
           }      
         }  /* nhstepm age range expressed in number of stepm */
         else /*= 0 Unknown */    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
           agev[m][i]=1;    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       }    /* if (stepm >= YEARM) hstepm=1;*/
        nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     }    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     for (i=1; i<=imx; i++)  {  
       for(m=1; (m<= maxwav); m++){    for (age=bage; age<=fage; age ++){ 
         if (s[m][i] > (nlstate+ndeath)) {      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
           printf("Error: Wrong value in nlstate or ndeath\n");        /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           goto end;      /* if (stepm >= YEARM) hstepm=1;*/
         }      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
       }  
     }      /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepma matrices, stored
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
       
     free_vector(severity,1,maxwav);      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     free_imatrix(outcome,1,maxwav+1,1,n);      
     free_vector(moisnais,1,n);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     free_vector(annais,1,n);      
     /* free_matrix(mint,1,maxwav,1,n);      printf("%d|",(int)age);fflush(stdout);
        free_matrix(anint,1,maxwav,1,n);*/      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     free_vector(moisdc,1,n);      
     free_vector(andc,1,n);      /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
            for(j=1; j<=nlstate;j++)
     wav=ivector(1,imx);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);            
                /* 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]);*/
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          }
   
       fprintf(ficreseij,"%3.0f",age );
       Tcode=ivector(1,100);      for(i=1; i<=nlstate;i++){
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        eip=0;
       ncodemax[1]=1;        for(j=1; j<=nlstate;j++){
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);          eip +=eij[i][j][(int)age];
                fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
    codtab=imatrix(1,100,1,10);        }
    h=0;        fprintf(ficreseij,"%9.4f", eip );
    m=pow(2,cptcoveff);      }
        fprintf(ficreseij,"\n");
    for(k=1;k<=cptcoveff; k++){      
      for(i=1; i <=(m/pow(2,k));i++){    }
        for(j=1; j <= ncodemax[k]; j++){    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    printf("\n");
            h++;    fprintf(ficlog,"\n");
            if (h>m) h=1;codtab[h][k]=j;    
          }  }
        }  
      }  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[] )
    }  
   {
     /* Covariances of health expectancies eij and of total life expectancies according
    /*for(i=1; i <=m ;i++){     to initial status i, ei. .
      for(k=1; k <=cptcovn; k++){    */
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
      }    int nhstepma, nstepma; /* Decreasing with age */
      printf("\n");    double age, agelim, hf;
    }    double ***p3matp, ***p3matm, ***varhe;
    scanf("%d",i);*/    double **dnewm,**doldm;
        double *xp, *xm;
    /* Calculates basic frequencies. Computes observed prevalence at single age    double **gp, **gm;
        and prints on file fileres'p'. */    double ***gradg, ***trgradg;
     int theta;
      
        double eip, vip;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    xp=vector(1,npar);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    xm=vector(1,npar);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    dnewm=matrix(1,nlstate*nlstate,1,npar);
          doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     /* 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] */    pstamp(ficresstdeij);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
     if(mle==1){    for(i=1; i<=nlstate;i++){
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);      for(j=1; j<=nlstate;j++)
     }        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
          fprintf(ficresstdeij," e%1d. ",i);
     /*--------- results files --------------*/    }
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);    fprintf(ficresstdeij,"\n");
    
     pstamp(ficrescveij);
    jk=1;    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
    fprintf(ficres,"# Parameters\n");    fprintf(ficrescveij,"# Age");
    printf("# Parameters\n");    for(i=1; i<=nlstate;i++)
    for(i=1,jk=1; i <=nlstate; i++){      for(j=1; j<=nlstate;j++){
      for(k=1; k <=(nlstate+ndeath); k++){        cptj= (j-1)*nlstate+i;
        if (k != i)        for(i2=1; i2<=nlstate;i2++)
          {          for(j2=1; j2<=nlstate;j2++){
            printf("%d%d ",i,k);            cptj2= (j2-1)*nlstate+i2;
            fprintf(ficres,"%1d%1d ",i,k);            if(cptj2 <= cptj)
            for(j=1; j <=ncovmodel; j++){              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
              printf("%f ",p[jk]);          }
              fprintf(ficres,"%f ",p[jk]);      }
              jk++;    fprintf(ficrescveij,"\n");
            }    
            printf("\n");    if(estepm < stepm){
            fprintf(ficres,"\n");      printf ("Problem %d lower than %d\n",estepm, stepm);
          }    }
      }    else  hstepm=estepm;   
    }    /* We compute the life expectancy from trapezoids spaced every estepm months
  if(mle==1){     * This is mainly to measure the difference between two models: for example
     /* Computing hessian and covariance matrix */     * if stepm=24 months pijx are given only every 2 years and by summing them
     ftolhess=ftol; /* Usually correct */     * we are calculating an estimate of the Life Expectancy assuming a linear 
     hesscov(matcov, p, npar, delti, ftolhess, func);     * progression in between and thus overestimating or underestimating according
  }     * to the curvature of the survival function. If, for the same date, we 
     fprintf(ficres,"# Scales\n");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     printf("# Scales\n");     * to compare the new estimate of Life expectancy with the same linear 
      for(i=1,jk=1; i <=nlstate; i++){     * hypothesis. A more precise result, taking into account a more precise
       for(j=1; j <=nlstate+ndeath; j++){     * curvature will be obtained if estepm is as small as stepm. */
         if (j!=i) {  
           fprintf(ficres,"%1d%1d",i,j);    /* For example we decided to compute the life expectancy with the smallest unit */
           printf("%1d%1d",i,j);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           for(k=1; k<=ncovmodel;k++){       nhstepm is the number of hstepm from age to agelim 
             printf(" %.5e",delti[jk]);       nstepm is the number of stepm from age to agelin. 
             fprintf(ficres," %.5e",delti[jk]);       Look at hpijx to understand the reason of that which relies in memory size
             jk++;       and note for a fixed period like estepm months */
           }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           printf("\n");       survival function given by stepm (the optimization length). Unfortunately it
           fprintf(ficres,"\n");       means that if the survival funtion is printed only each two years of age and if
         }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       }       results. So we changed our mind and took the option of the best precision.
      }    */
        hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     k=1;  
     fprintf(ficres,"# Covariance\n");    /* If stepm=6 months */
     printf("# Covariance\n");    /* nhstepm age range expressed in number of stepm */
     for(i=1;i<=npar;i++){    agelim=AGESUP;
       /*  if (k>nlstate) k=1;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
       i1=(i-1)/(ncovmodel*nlstate)+1;    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    /* if (stepm >= YEARM) hstepm=1;*/
       printf("%s%d%d",alph[k],i1,tab[i]);*/    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       fprintf(ficres,"%3d",i);    
       printf("%3d",i);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(j=1; j<=i;j++){    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficres," %.5e",matcov[i][j]);    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
         printf(" %.5e",matcov[i][j]);    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
       }    gp=matrix(0,nhstepm,1,nlstate*nlstate);
       fprintf(ficres,"\n");    gm=matrix(0,nhstepm,1,nlstate*nlstate);
       printf("\n");  
       k++;    for (age=bage; age<=fage; age ++){ 
     }      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
          /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     while((c=getc(ficpar))=='#' && c!= EOF){      /* if (stepm >= YEARM) hstepm=1;*/
       ungetc(c,ficpar);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
       fgets(line, MAXLINE, ficpar);  
       puts(line);      /* If stepm=6 months */
       fputs(line,ficparo);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
     }         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     ungetc(c,ficpar);      
        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);  
          /* Computing  Variances of health expectancies */
     if (fage <= 2) {      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
       bage = agemin;         decrease memory allocation */
       fage = agemaxpar;      for(theta=1; theta <=npar; theta++){
     }        for(i=1; i<=npar; i++){ 
              xp[i] = x[i] + (i==theta ?delti[theta]:0);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          xm[i] = x[i] - (i==theta ?delti[theta]:0);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);        }
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
          hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);        for(j=1; j<= nlstate; j++){
     fgets(line, MAXLINE, ficpar);          for(i=1; i<=nlstate; i++){
     puts(line);            for(h=0; h<=nhstepm-1; h++){
     fputs(line,ficparo);              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.;
   ungetc(c,ficpar);            }
            }
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        }
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        for(ij=1; ij<= nlstate*nlstate; ij++)
                for(h=0; h<=nhstepm-1; h++){
   while((c=getc(ficpar))=='#' && c!= EOF){            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);      }/* End theta */
     puts(line);      
     fputs(line,ficparo);      
   }      for(h=0; h<=nhstepm-1; h++)
   ungetc(c,ficpar);        for(j=1; j<=nlstate*nlstate;j++)
            for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
    dateprev1=anprev1+mprev1/12.+jprev1/365.;      
    dateprev2=anprev2+mprev2/12.+jprev2/365.;  
        for(ij=1;ij<=nlstate*nlstate;ij++)
   fscanf(ficpar,"pop_based=%d\n",&popbased);        for(ji=1;ji<=nlstate*nlstate;ji++)
   fprintf(ficparo,"pop_based=%d\n",popbased);            varhe[ij][ji][(int)age] =0.;
   fprintf(ficres,"pop_based=%d\n",popbased);    
         printf("%d|",(int)age);fflush(stdout);
   while((c=getc(ficpar))=='#' && c!= EOF){       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     ungetc(c,ficpar);       for(h=0;h<=nhstepm-1;h++){
     fgets(line, MAXLINE, ficpar);        for(k=0;k<=nhstepm-1;k++){
     puts(line);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     fputs(line,ficparo);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   }          for(ij=1;ij<=nlstate*nlstate;ij++)
   ungetc(c,ficpar);            for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);        }
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);      }
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  
       /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
 while((c=getc(ficpar))=='#' && c!= EOF){      for(i=1; i<=nlstate;i++)
     ungetc(c,ficpar);        for(j=1; j<=nlstate;j++)
     fgets(line, MAXLINE, ficpar);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     puts(line);            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
     fputs(line,ficparo);            
   }            /* 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]);*/
   ungetc(c,ficpar);  
           }
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);  
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      fprintf(ficresstdeij,"%3.0f",age );
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      for(i=1; i<=nlstate;i++){
         eip=0.;
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        vip=0.;
         for(j=1; j<=nlstate;j++){
 /*------------ gnuplot -------------*/          eip += eij[i][j][(int)age];
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
              vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
 /*------------ free_vector  -------------*/          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
  chdir(path);        }
          fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
  free_ivector(wav,1,imx);      }
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      fprintf(ficresstdeij,"\n");
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    
  free_ivector(num,1,n);      fprintf(ficrescveij,"%3.0f",age );
  free_vector(agedc,1,n);      for(i=1; i<=nlstate;i++)
  /*free_matrix(covar,1,NCOVMAX,1,n);*/        for(j=1; j<=nlstate;j++){
  fclose(ficparo);          cptj= (j-1)*nlstate+i;
  fclose(ficres);          for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
 /*--------- index.htm --------*/              cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
          }
   /*--------------- Prevalence limit --------------*/      fprintf(ficrescveij,"\n");
       
   strcpy(filerespl,"pl");    }
   strcat(filerespl,fileres);    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   }    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fprintf(ficrespl,"#Prevalence limit\n");    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fprintf(ficrespl,"#Age ");    printf("\n");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    fprintf(ficlog,"\n");
   fprintf(ficrespl,"\n");  
      free_vector(xm,1,npar);
   prlim=matrix(1,nlstate,1,nlstate);    free_vector(xp,1,npar);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  }
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;  /************ Variance ******************/
   agebase=agemin;  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[])
   agelim=agemaxpar;  {
   ftolpl=1.e-10;    /* Variance of health expectancies */
   i1=cptcoveff;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   if (cptcovn < 1){i1=1;}    /* double **newm;*/
     double **dnewm,**doldm;
   for(cptcov=1;cptcov<=i1;cptcov++){    double **dnewmp,**doldmp;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int i, j, nhstepm, hstepm, h, nstepm ;
         k=k+1;    int k, cptcode;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    double *xp;
         fprintf(ficrespl,"\n#******");    double **gp, **gm;  /* for var eij */
         for(j=1;j<=cptcoveff;j++)    double ***gradg, ***trgradg; /*for var eij */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double **gradgp, **trgradgp; /* for var p point j */
         fprintf(ficrespl,"******\n");    double *gpp, *gmp; /* for var p point j */
            double **varppt; /* for var p point j nlstate to nlstate+ndeath */
         for (age=agebase; age<=agelim; age++){    double ***p3mat;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    double age,agelim, hf;
           fprintf(ficrespl,"%.0f",age );    double ***mobaverage;
           for(i=1; i<=nlstate;i++)    int theta;
           fprintf(ficrespl," %.5f", prlim[i][i]);    char digit[4];
           fprintf(ficrespl,"\n");    char digitp[25];
         }  
       }    char fileresprobmorprev[FILENAMELENGTH];
     }  
   fclose(ficrespl);    if(popbased==1){
       if(mobilav!=0)
   /*------------- h Pij x at various ages ------------*/        strcpy(digitp,"-populbased-mobilav-");
        else strcpy(digitp,"-populbased-nomobil-");
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    else 
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      strcpy(digitp,"-stablbased-");
   }  
   printf("Computing pij: result on file '%s' \n", filerespij);    if (mobilav!=0) {
        mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   stepsize=(int) (stepm+YEARM-1)/YEARM;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   /*if (stepm<=24) stepsize=2;*/        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
   agelim=AGESUP;      }
   hstepm=stepsize*YEARM; /* Every year of age */    }
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  
      strcpy(fileresprobmorprev,"prmorprev"); 
   k=0;    sprintf(digit,"%-d",ij);
   for(cptcov=1;cptcov<=i1;cptcov++){    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       k=k+1;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         fprintf(ficrespij,"\n#****** ");    strcat(fileresprobmorprev,fileres);
         for(j=1;j<=cptcoveff;j++)    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
         fprintf(ficrespij,"******\n");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
            }
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    pstamp(ficresprobmorprev);
           oldm=oldms;savm=savms;    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);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
           fprintf(ficrespij,"# Age");    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           for(i=1; i<=nlstate;i++)      fprintf(ficresprobmorprev," p.%-d SE",j);
             for(j=1; j<=nlstate+ndeath;j++)      for(i=1; i<=nlstate;i++)
               fprintf(ficrespij," %1d-%1d",i,j);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
           fprintf(ficrespij,"\n");    }  
           for (h=0; h<=nhstepm; h++){    fprintf(ficresprobmorprev,"\n");
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    fprintf(ficgp,"\n# Routine varevsij");
             for(i=1; i<=nlstate;i++)    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
               for(j=1; j<=nlstate+ndeath;j++)    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(ficrespij," %.5f", p3mat[i][j][h]);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
             fprintf(ficrespij,"\n");  /*   } */
           }    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    pstamp(ficresvij);
           fprintf(ficrespij,"\n");    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
         }    if(popbased==1)
     }      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
   }    else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
   fclose(ficrespij);      for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   /*---------- Forecasting ------------------*/  
   if((stepm == 1) && (model==".")){    xp=vector(1,npar);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    dnewm=matrix(1,nlstate,1,npar);
 if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    doldm=matrix(1,nlstate,1,nlstate);
     free_matrix(mint,1,maxwav,1,n);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_vector(weight,1,n);}  
   else{    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     erreur=108;    gpp=vector(nlstate+1,nlstate+ndeath);
     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);    gmp=vector(nlstate+1,nlstate+ndeath);
   }    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
      
     if(estepm < stepm){
   /*---------- Health expectancies and variances ------------*/      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
   strcpy(filerest,"t");    else  hstepm=estepm;   
   strcat(filerest,fileres);    /* For example we decided to compute the life expectancy with the smallest unit */
   if((ficrest=fopen(filerest,"w"))==NULL) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;       nhstepm is the number of hstepm from age to agelim 
   }       nstepm is the number of stepm from age to agelin. 
   printf("Computing Total LEs with variances: file '%s' \n", filerest);       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
        survival function given by stepm (the optimization length). Unfortunately it
   strcpy(filerese,"e");       means that if the survival funtion is printed every two years of age and if
   strcat(filerese,fileres);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   if((ficreseij=fopen(filerese,"w"))==NULL) {       results. So we changed our mind and took the option of the best precision.
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    */
   }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
  strcpy(fileresv,"v");      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   strcat(fileresv,fileres);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   }      gp=matrix(0,nhstepm,1,nlstate);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      gm=matrix(0,nhstepm,1,nlstate);
   
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){      for(theta=1; theta <=npar; theta++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       k=k+1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fprintf(ficrest,"\n#****** ");        }
       for(j=1;j<=cptcoveff;j++)        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       fprintf(ficrest,"******\n");  
         if (popbased==1) {
       fprintf(ficreseij,"\n#****** ");          if(mobilav ==0){
       for(j=1;j<=cptcoveff;j++)            for(i=1; i<=nlstate;i++)
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);              prlim[i][i]=probs[(int)age][i][ij];
       fprintf(ficreseij,"******\n");          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
       fprintf(ficresvij,"\n#****** ");              prlim[i][i]=mobaverage[(int)age][i][ij];
       for(j=1;j<=cptcoveff;j++)          }
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        }
       fprintf(ficresvij,"******\n");    
         for(j=1; j<= nlstate; j++){
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          for(h=0; h<=nhstepm; h++){
       oldm=oldms;savm=savms;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);                gp[h][j] += prlim[i][i]*p3mat[i][j][h];
       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);        /* This for computing probability of death (h=1 means
               computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
          */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
       fprintf(ficrest,"\n");            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
       hf=1;        /* end probability of death */
       if (stepm >= YEARM) hf=stepm/YEARM;  
       epj=vector(1,nlstate+1);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
       for(age=bage; age <=fage ;age++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         if (popbased==1) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           for(i=1; i<=nlstate;i++)   
             prlim[i][i]=probs[(int)age][i][k];        if (popbased==1) {
         }          if(mobilav ==0){
                    for(i=1; i<=nlstate;i++)
         fprintf(ficrest," %.0f",age);              prlim[i][i]=probs[(int)age][i][ij];
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          }else{ /* mobilav */ 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {            for(i=1; i<=nlstate;i++)
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];              prlim[i][i]=mobaverage[(int)age][i][ij];
           }          }
           epj[nlstate+1] +=epj[j];        }
         }  
         for(i=1, vepp=0.;i <=nlstate;i++)        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
           for(j=1;j <=nlstate;j++)          for(h=0; h<=nhstepm; h++){
             vepp += vareij[i][j][(int)age];            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
         for(j=1;j <=nlstate;j++){          }
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));        }
         }        /* This for computing probability of death (h=1 means
         fprintf(ficrest,"\n");           computed over hstepm matrices product = hstepm*stepm months) 
       }           as a weighted average of prlim.
     }        */
   }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
   fclose(ficreseij);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   fclose(ficresvij);        }    
   fclose(ficrest);        /* end probability of death */
   fclose(ficpar);  
   free_vector(epj,1,nlstate+1);        for(j=1; j<= nlstate; j++) /* vareij */
            for(h=0; h<=nhstepm; h++){
   /*------- Variance limit prevalence------*/              gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   strcpy(fileresvpl,"vpl");  
   strcat(fileresvpl,fileres);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        }
     exit(0);  
   }      } /* End theta */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){      for(h=0; h<=nhstepm; h++) /* veij */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(j=1; j<=nlstate;j++)
       k=k+1;          for(theta=1; theta <=npar; theta++)
       fprintf(ficresvpl,"\n#****** ");            trgradg[h][j][theta]=gradg[h][theta][j];
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       fprintf(ficresvpl,"******\n");        for(theta=1; theta <=npar; theta++)
                trgradgp[j][theta]=gradgp[theta][j];
       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);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     }      for(i=1;i<=nlstate;i++)
  }        for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   fclose(ficresvpl);  
       for(h=0;h<=nhstepm;h++){
   /*---------- End : free ----------------*/        for(k=0;k<=nhstepm;k++){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          for(i=1;i<=nlstate;i++)
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);            for(j=1;j<=nlstate;j++)
                vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
          }
   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);      /* pptj */
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
        matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   free_matrix(matcov,1,npar,1,npar);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   free_vector(delti,1,npar);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   free_matrix(agev,1,maxwav,1,imx);          varppt[j][i]=doldmp[j][i];
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      /* end ppptj */
       /*  x centered again */
   if(erreur >0)      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     printf("End of Imach with error %d\n",erreur);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   else   printf("End of Imach\n");   
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      if (popbased==1) {
          if(mobilav ==0){
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/          for(i=1; i<=nlstate;i++)
   /*printf("Total time was %d uSec.\n", total_usecs);*/            prlim[i][i]=probs[(int)age][i][ij];
   /*------ End -----------*/        }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
  end:        }
 #ifdef windows      }
   /* chdir(pathcd);*/               
 #endif      /* This for computing probability of death (h=1 means
  /*system("wgnuplot graph.plt");*/         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
  /*system("../gp37mgw/wgnuplot graph.plt");*/         as a weighted average of prlim.
  /*system("cd ../gp37mgw");*/      */
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/      for(j=nlstate+1;j<=nlstate+ndeath;j++){
  strcpy(plotcmd,GNUPLOTPROGRAM);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
  strcat(plotcmd," ");          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
  strcat(plotcmd,optionfilegnuplot);      }    
  system(plotcmd);      /* end probability of death */
   
 #ifdef windows      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   while (z[0] != 'q') {      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     chdir(path);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     printf("\nType e to edit output files, c to start again, and q for exiting: ");        for(i=1; i<=nlstate;i++){
     scanf("%s",z);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     if (z[0] == 'c') system("./imach");        }
     else if (z[0] == 'e') {      } 
       chdir(path);      fprintf(ficresprobmorprev,"\n");
       system(optionfilehtm);  
     }      fprintf(ficresvij,"%.0f ",age );
     else if (z[0] == 'q') exit(0);      for(i=1; i<=nlstate;i++)
   }        for(j=1; j<=nlstate;j++){
 #endif          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 size 320, 240");
     /* 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 lt 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 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, first2;
     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+1];
     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; */
     tj = (int) pow(2,cptcoveff);
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(j1=1; j1<=tj;j1++){
       /*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#");    
         }
         
         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 (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
                                                            * 1  1 1 1 1
                                                            * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           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]]];
           
       
           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);
   
           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++;
               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++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 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 */
         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);
         
         /* 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;first2=2;
         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) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d 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. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d 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. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* 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 size 320, 240");
                       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=pow(2,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%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.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%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.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=pow(2,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 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        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 size 320, 240\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 lt 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 lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 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 size 320, 240\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 lt 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 lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 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 size 320, 240\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 size 320, 240\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");
           }
         }
       }
      }
     /*goto avoid;*/
      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 size 320, 240\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;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*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 */
    avoid:
      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 size 320, 240\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 %d 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 %d 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.",dummy) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d 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 %d 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 %d 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 %d 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.", dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d 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 %d 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 %d 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 %d 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 %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%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 '%ld' at line number %d 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 '%ld' at line number %d 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 '%ld' at line number %d 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 '%ld' at line number %d 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);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ = *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int i1, j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       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;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* 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]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(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 */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; 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--;
             cutl(stre,strb,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 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,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 */
             cutl(strc,strb,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*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=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 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* 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);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         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(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\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]="1234";
     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++;
       fputs(line,stdout);
       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++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     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) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     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 guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         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);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         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);
   
       /* Reads covariance matrix */
       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++;
         fputs(line,stdout);
         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,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* 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,NCOVMAX); /* Gives the position of a product */
     /* 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,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* 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;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-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 ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); 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)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     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);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ 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");
       fprintf(ficgp,"set datafile 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);
         fputs(line,stdout);
         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);
         fputs(line,stdout);
         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);
         fputs(line,stdout);
         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);
         fputs(line,stdout);
         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) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       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++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           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++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           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);  
           /*
            */
           /* goto endfree; */
    
           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; /* Segmentation fault */
             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,NCOVMAX,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++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           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); /*here or after loop ? */
       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,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       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 %ld 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 %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.30  
changed lines
  Added in v.1.145


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