Diff for /imach/src/imach.c between versions 1.46 and 1.152

version 1.46, 2002/05/30 17:44:35 version 1.152, 2014/06/18 17:54:09
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.152  2014/06/18 17:54:09  brouard
      Summary: open browser, use gnuplot on same dir than imach if not found in the path
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.151  2014/06/18 16:43:30  brouard
   first survey ("cross") where individuals from different ages are    *** empty log message ***
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.150  2014/06/18 16:42:35  brouard
   second wave of interviews ("longitudinal") which measure each change    Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
   (if any) in individual health status.  Health expectancies are    Author: brouard
   computed from the time spent in each health state according to a  
   model. More health states you consider, more time is necessary to reach the    Revision 1.149  2014/06/18 15:51:14  brouard
   Maximum Likelihood of the parameters involved in the model.  The    Summary: Some fixes in parameter files errors
   simplest model is the multinomial logistic model where pij is the    Author: Nicolas Brouard
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.148  2014/06/17 17:38:48  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Summary: Nothing new
   'age' is age and 'sex' is a covariate. If you want to have a more    Author: Brouard
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Just a new packaging for OS/X version 0.98nS
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.147  2014/06/16 10:33:11  brouard
     *** empty log message ***
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.146  2014/06/16 10:20:28  brouard
   identical for each individual. Also, if a individual missed an    Summary: Merge
   intermediate interview, the information is lost, but taken into    Author: Brouard
   account using an interpolation or extrapolation.    
     Merge, before building revised version.
   hPijx is the probability to be observed in state i at age x+h  
   conditional to the observed state i at age x. The delay 'h' can be    Revision 1.145  2014/06/10 21:23:15  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    Summary: Debugging with valgrind
   states. This elementary transition (by month or quarter trimester,    Author: Nicolas Brouard
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Lot of changes in order to output the results with some covariates
   and the contribution of each individual to the likelihood is simply    After the Edimburgh REVES conference 2014, it seems mandatory to
   hPijx.    improve the code.
     No more memory valgrind error but a lot has to be done in order to
   Also this programme outputs the covariance matrix of the parameters but also    continue the work of splitting the code into subroutines.
   of the life expectancies. It also computes the prevalence limits.    Also, decodemodel has been improved. Tricode is still not
      optimal. nbcode should be improved. Documentation has been added in
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    the source code.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.143  2014/01/26 09:45:38  brouard
   from the European Union.    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   can be accessed at http://euroreves.ined.fr/imach .    (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   **********************************************************************/  
      Revision 1.142  2014/01/26 03:57:36  brouard
 #include <math.h>    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
 #include <stdio.h>  
 #include <stdlib.h>    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #include <unistd.h>  
     Revision 1.141  2014/01/26 02:42:01  brouard
 #define MAXLINE 256    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
 #define GNUPLOTPROGRAM "gnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.140  2011/09/02 10:37:54  brouard
 #define FILENAMELENGTH 80    Summary: times.h is ok with mingw32 now.
 /*#define DEBUG*/  
 #define windows    Revision 1.139  2010/06/14 07:50:17  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Revision 1.138  2010/04/30 18:19:40  brouard
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    *** empty log message ***
   
 #define NINTERVMAX 8    Revision 1.137  2010/04/29 18:11:38  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    (Module): Checking covariates for more complex models
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    than V1+V2. A lot of change to be done. Unstable.
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.136  2010/04/26 20:30:53  brouard
 #define YEARM 12. /* Number of months per year */    (Module): merging some libgsl code. Fixing computation
 #define AGESUP 130    of likelione (using inter/intrapolation if mle = 0) in order to
 #define AGEBASE 40    get same likelihood as if mle=1.
     Some cleaning of code and comments added.
   
 int erreur; /* Error number */    Revision 1.135  2009/10/29 15:33:14  brouard
 int nvar;    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.134  2009/10/29 13:18:53  brouard
 int nlstate=2; /* Number of live states */    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.133  2009/07/06 10:21:25  brouard
 int popbased=0;    just nforces
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.132  2009/07/06 08:22:05  brouard
 int maxwav; /* Maxim number of waves */    Many tings
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.131  2009/06/20 16:22:47  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Some dimensions resccaled
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.130  2009/05/26 06:44:34  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    (Module): Max Covariate is now set to 20 instead of 8. A
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    lot of cleaning with variables initialized to 0. Trying to make
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  
 FILE *ficreseij;    Revision 1.129  2007/08/31 13:49:27  lievre
   char filerese[FILENAMELENGTH];    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Revision 1.128  2006/06/30 13:02:05  brouard
  FILE  *ficresvpl;    (Module): Clarifications on computing e.j
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.127  2006/04/28 18:11:50  brouard
 #define NR_END 1    (Module): Yes the sum of survivors was wrong since
 #define FREE_ARG char*    imach-114 because nhstepm was no more computed in the age
 #define FTOL 1.0e-10    loop. Now we define nhstepma in the age loop.
     (Module): In order to speed up (in case of numerous covariates) we
 #define NRANSI    compute health expectancies (without variances) in a first step
 #define ITMAX 200    and then all the health expectancies with variances or standard
     deviation (needs data from the Hessian matrices) which slows the
 #define TOL 2.0e-4    computation.
     In the future we should be able to stop the program is only health
 #define CGOLD 0.3819660    expectancies and graph are needed without standard deviations.
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.126  2006/04/28 17:23:28  brouard
     (Module): Yes the sum of survivors was wrong since
 #define GOLD 1.618034    imach-114 because nhstepm was no more computed in the age
 #define GLIMIT 100.0    loop. Now we define nhstepma in the age loop.
 #define TINY 1.0e-20    Version 0.98h
   
 static double maxarg1,maxarg2;    Revision 1.125  2006/04/04 15:20:31  lievre
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Errors in calculation of health expectancies. Age was not initialized.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Forecasting file added.
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.124  2006/03/22 17:13:53  lievre
 #define rint(a) floor(a+0.5)    Parameters are printed with %lf instead of %f (more numbers after the comma).
     The log-likelihood is printed in the log file
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.123  2006/03/20 10:52:43  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    * imach.c (Module): <title> changed, corresponds to .htm file
     name. <head> headers where missing.
 int imx;  
 int stepm;    * imach.c (Module): Weights can have a decimal point as for
 /* Stepm, step in month: minimum step interpolation*/    English (a comma might work with a correct LC_NUMERIC environment,
     otherwise the weight is truncated).
 int estepm;    Modification of warning when the covariates values are not 0 or
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    1.
     Version 0.98g
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.122  2006/03/20 09:45:41  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    (Module): Weights can have a decimal point as for
 double **pmmij, ***probs, ***mobaverage;    English (a comma might work with a correct LC_NUMERIC environment,
 double dateintmean=0;    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 double *weight;    1.
 int **s; /* Status */    Version 0.98g
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.121  2006/03/16 17:45:01  lievre
     * imach.c (Module): Comments concerning covariates added
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    * imach.c (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
 /**************** split *************************/    not 1 month. Version 0.98f
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Revision 1.120  2006/03/16 15:10:38  lievre
    char *s;                             /* pointer */    (Module): refinements in the computation of lli if
    int  l1, l2;                         /* length counters */    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.119  2006/03/15 17:42:26  brouard
 #ifdef windows    (Module): Bug if status = -2, the loglikelihood was
    s = strrchr( path, '\\' );           /* find last / */    computed as likelihood omitting the logarithm. Version O.98e
 #else  
    s = strrchr( path, '/' );            /* find last / */    Revision 1.118  2006/03/14 18:20:07  brouard
 #endif    (Module): varevsij Comments added explaining the second
    if ( s == NULL ) {                   /* no directory, so use current */    table of variances if popbased=1 .
 #if     defined(__bsd__)                /* get current working directory */    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
       extern char       *getwd( );    (Module): Function pstamp added
     (Module): Version 0.98d
       if ( getwd( dirc ) == NULL ) {  
 #else    Revision 1.117  2006/03/14 17:16:22  brouard
       extern char       *getcwd( );    (Module): varevsij Comments added explaining the second
     table of variances if popbased=1 .
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #endif    (Module): Function pstamp added
          return( GLOCK_ERROR_GETCWD );    (Module): Version 0.98d
       }  
       strcpy( name, path );             /* we've got it */    Revision 1.116  2006/03/06 10:29:27  brouard
    } else {                             /* strip direcotry from path */    (Module): Variance-covariance wrong links and
       s++;                              /* after this, the filename */    varian-covariance of ej. is needed (Saito).
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.115  2006/02/27 12:17:45  brouard
       strcpy( name, s );                /* save file name */    (Module): One freematrix added in mlikeli! 0.98c
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.114  2006/02/26 12:57:58  brouard
    }    (Module): Some improvements in processing parameter
    l1 = strlen( dirc );                 /* length of directory */    filename with strsep.
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.113  2006/02/24 14:20:24  brouard
 #else    (Module): Memory leaks checks with valgrind and:
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    datafile was not closed, some imatrix were not freed and on matrix
 #endif    allocation too.
    s = strrchr( name, '.' );            /* find last / */  
    s++;    Revision 1.112  2006/01/30 09:55:26  brouard
    strcpy(ext,s);                       /* save extension */    (Module): Back to gnuplot.exe instead of wgnuplot.exe
    l1= strlen( name);  
    l2= strlen( s)+1;    Revision 1.111  2006/01/25 20:38:18  brouard
    strncpy( finame, name, l1-l2);    (Module): Lots of cleaning and bugs added (Gompertz)
    finame[l1-l2]= 0;    (Module): Comments can be added in data file. Missing date values
    return( 0 );                         /* we're done */    can be a simple dot '.'.
 }  
     Revision 1.110  2006/01/25 00:51:50  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
 /******************************************/  
     Revision 1.109  2006/01/24 19:37:15  brouard
 void replace(char *s, char*t)    (Module): Comments (lines starting with a #) are allowed in data.
 {  
   int i;    Revision 1.108  2006/01/19 18:05:42  lievre
   int lg=20;    Gnuplot problem appeared...
   i=0;    To be fixed
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.107  2006/01/19 16:20:37  brouard
     (s[i] = t[i]);    Test existence of gnuplot in imach path
     if (t[i]== '\\') s[i]='/';  
   }    Revision 1.106  2006/01/19 13:24:36  brouard
 }    Some cleaning and links added in html output
   
 int nbocc(char *s, char occ)    Revision 1.105  2006/01/05 20:23:19  lievre
 {    *** empty log message ***
   int i,j=0;  
   int lg=20;    Revision 1.104  2005/09/30 16:11:43  lievre
   i=0;    (Module): sump fixed, loop imx fixed, and simplifications.
   lg=strlen(s);    (Module): If the status is missing at the last wave but we know
   for(i=0; i<= lg; i++) {    that the person is alive, then we can code his/her status as -2
   if  (s[i] == occ ) j++;    (instead of missing=-1 in earlier versions) and his/her
   }    contributions to the likelihood is 1 - Prob of dying from last
   return j;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 }    the healthy state at last known wave). Version is 0.98
   
 void cutv(char *u,char *v, char*t, char occ)    Revision 1.103  2005/09/30 15:54:49  lievre
 {    (Module): sump fixed, loop imx fixed, and simplifications.
   int i,lg,j,p=0;  
   i=0;    Revision 1.102  2004/09/15 17:31:30  brouard
   for(j=0; j<=strlen(t)-1; j++) {    Add the possibility to read data file including tab characters.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    Revision 1.101  2004/09/15 10:38:38  brouard
     Fix on curr_time
   lg=strlen(t);  
   for(j=0; j<p; j++) {    Revision 1.100  2004/07/12 18:29:06  brouard
     (u[j] = t[j]);    Add version for Mac OS X. Just define UNIX in Makefile
   }  
      u[p]='\0';    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    Revision 1.98  2004/05/16 15:05:56  brouard
   }    New version 0.97 . First attempt to estimate force of mortality
 }    directly from the data i.e. without the need of knowing the health
     state at each age, but using a Gompertz model: log u =a + b*age .
 /********************** nrerror ********************/    This is the basic analysis of mortality and should be done before any
     other analysis, in order to test if the mortality estimated from the
 void nrerror(char error_text[])    cross-longitudinal survey is different from the mortality estimated
 {    from other sources like vital statistic data.
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);    The same imach parameter file can be used but the option for mle should be -3.
   exit(1);  
 }    Agnès, who wrote this part of the code, tried to keep most of the
 /*********************** vector *******************/    former routines in order to include the new code within the former code.
 double *vector(int nl, int nh)  
 {    The output is very simple: only an estimate of the intercept and of
   double *v;    the slope with 95% confident intervals.
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");    Current limitations:
   return v-nl+NR_END;    A) Even if you enter covariates, i.e. with the
 }    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
     B) There is no computation of Life Expectancy nor Life Table.
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    Revision 1.97  2004/02/20 13:25:42  lievre
 {    Version 0.96d. Population forecasting command line is (temporarily)
   free((FREE_ARG)(v+nl-NR_END));    suppressed.
 }  
     Revision 1.96  2003/07/15 15:38:55  brouard
 /************************ivector *******************************/    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 int *ivector(long nl,long nh)    rewritten within the same printf. Workaround: many printfs.
 {  
   int *v;    Revision 1.95  2003/07/08 07:54:34  brouard
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    * imach.c (Repository):
   if (!v) nrerror("allocation failure in ivector");    (Repository): Using imachwizard code to output a more meaningful covariance
   return v-nl+NR_END;    matrix (cov(a12,c31) instead of numbers.
 }  
     Revision 1.94  2003/06/27 13:00:02  brouard
 /******************free ivector **************************/    Just cleaning
 void free_ivector(int *v, long nl, long nh)  
 {    Revision 1.93  2003/06/25 16:33:55  brouard
   free((FREE_ARG)(v+nl-NR_END));    (Module): On windows (cygwin) function asctime_r doesn't
 }    exist so I changed back to asctime which exists.
     (Module): Version 0.96b
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)    Revision 1.92  2003/06/25 16:30:45  brouard
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    (Module): On windows (cygwin) function asctime_r doesn't
 {    exist so I changed back to asctime which exists.
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    Revision 1.91  2003/06/25 15:30:29  brouard
      * imach.c (Repository): Duplicated warning errors corrected.
   /* allocate pointers to rows */    (Repository): Elapsed time after each iteration is now output. It
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    helps to forecast when convergence will be reached. Elapsed time
   if (!m) nrerror("allocation failure 1 in matrix()");    is stamped in powell.  We created a new html file for the graphs
   m += NR_END;    concerning matrix of covariance. It has extension -cov.htm.
   m -= nrl;  
      Revision 1.90  2003/06/24 12:34:15  brouard
      (Module): Some bugs corrected for windows. Also, when
   /* allocate rows and set pointers to them */    mle=-1 a template is output in file "or"mypar.txt with the design
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    of the covariance matrix to be input.
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    Revision 1.89  2003/06/24 12:30:52  brouard
   m[nrl] -= ncl;    (Module): Some bugs corrected for windows. Also, when
      mle=-1 a template is output in file "or"mypar.txt with the design
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    of the covariance matrix to be input.
    
   /* return pointer to array of pointers to rows */    Revision 1.88  2003/06/23 17:54:56  brouard
   return m;    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
 }  
     Revision 1.87  2003/06/18 12:26:01  brouard
 /****************** free_imatrix *************************/    Version 0.96
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;    Revision 1.86  2003/06/17 20:04:08  brouard
       long nch,ncl,nrh,nrl;    (Module): Change position of html and gnuplot routines and added
      /* free an int matrix allocated by imatrix() */    routine fileappend.
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    Revision 1.85  2003/06/17 13:12:43  brouard
   free((FREE_ARG) (m+nrl-NR_END));    * imach.c (Repository): Check when date of death was earlier that
 }    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
 /******************* matrix *******************************/    was wrong (infinity). We still send an "Error" but patch by
 double **matrix(long nrl, long nrh, long ncl, long nch)    assuming that the date of death was just one stepm after the
 {    interview.
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    (Repository): Because some people have very long ID (first column)
   double **m;    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    truncation)
   if (!m) nrerror("allocation failure 1 in matrix()");    (Repository): No more line truncation errors.
   m += NR_END;  
   m -= nrl;    Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    place. It differs from routine "prevalence" which may be called
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    many times. Probs is memory consuming and must be used with
   m[nrl] += NR_END;    parcimony.
   m[nrl] -= ncl;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Revision 1.83  2003/06/10 13:39:11  lievre
   return m;    *** empty log message ***
 }  
     Revision 1.82  2003/06/05 15:57:20  brouard
 /*************************free matrix ************************/    Add log in  imach.c and  fullversion number is now printed.
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  
 {  */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  /*
   free((FREE_ARG)(m+nrl-NR_END));     Interpolated Markov Chain
 }  
     Short summary of the programme:
 /******************* ma3x *******************************/    
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    This program computes Healthy Life Expectancies from
 {    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    first survey ("cross") where individuals from different ages are
   double ***m;    interviewed on their health status or degree of disability (in the
     case of a health survey which is our main interest) -2- at least a
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    second wave of interviews ("longitudinal") which measure each change
   if (!m) nrerror("allocation failure 1 in matrix()");    (if any) in individual health status.  Health expectancies are
   m += NR_END;    computed from the time spent in each health state according to a
   m -= nrl;    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    simplest model is the multinomial logistic model where pij is the
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    probability to be observed in state j at the second wave
   m[nrl] += NR_END;    conditional to be observed in state i at the first wave. Therefore
   m[nrl] -= ncl;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     'age' is age and 'sex' is a covariate. If you want to have a more
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    you to do it.  More covariates you add, slower the
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    convergence.
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;    The advantage of this computer programme, compared to a simple
   for (j=ncl+1; j<=nch; j++)    multinomial logistic model, is clear when the delay between waves is not
     m[nrl][j]=m[nrl][j-1]+nlay;    identical for each individual. Also, if a individual missed an
      intermediate interview, the information is lost, but taken into
   for (i=nrl+1; i<=nrh; i++) {    account using an interpolation or extrapolation.  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    hPijx is the probability to be observed in state i at age x+h
       m[i][j]=m[i][j-1]+nlay;    conditional to the observed state i at age x. The delay 'h' can be
   }    split into an exact number (nh*stepm) of unobserved intermediate
   return m;    states. This elementary transition (by month, quarter,
 }    semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
 /*************************free ma3x ************************/    and the contribution of each individual to the likelihood is simply
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    hPijx.
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    Also this programme outputs the covariance matrix of the parameters but also
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    of the life expectancies. It also computes the period (stable) prevalence. 
   free((FREE_ARG)(m+nrl-NR_END));    
 }    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
 /***************** f1dim *************************/    This software have been partly granted by Euro-REVES, a concerted action
 extern int ncom;    from the European Union.
 extern double *pcom,*xicom;    It is copyrighted identically to a GNU software product, ie programme and
 extern double (*nrfunc)(double []);    software can be distributed freely for non commercial use. Latest version
      can be accessed at http://euroreves.ined.fr/imach .
 double f1dim(double x)  
 {    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   int j;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   double f;    
   double *xt;    **********************************************************************/
    /*
   xt=vector(1,ncom);    main
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    read parameterfile
   f=(*nrfunc)(xt);    read datafile
   free_vector(xt,1,ncom);    concatwav
   return f;    freqsummary
 }    if (mle >= 1)
       mlikeli
 /*****************brent *************************/    print results files
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    if mle==1 
 {       computes hessian
   int iter;    read end of parameter file: agemin, agemax, bage, fage, estepm
   double a,b,d,etemp;        begin-prev-date,...
   double fu,fv,fw,fx;    open gnuplot file
   double ftemp;    open html file
   double p,q,r,tol1,tol2,u,v,w,x,xm;    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
   double e=0.0;     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
                                      | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
   a=(ax < cx ? ax : cx);      freexexit2 possible for memory heap.
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;    h Pij x                         | pij_nom  ficrestpij
   fw=fv=fx=(*f)(x);     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
   for (iter=1;iter<=ITMAX;iter++) {         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
     xm=0.5*(a+b);         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
     printf(".");fflush(stdout);         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
 #ifdef DEBUG    variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
     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);     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    forecasting if prevfcast==1 prevforecast call prevalence()
       *xmin=x;    health expectancies
       return fx;    Variance-covariance of DFLE
     }    prevalence()
     ftemp=fu;     movingaverage()
     if (fabs(e) > tol1) {    varevsij() 
       r=(x-w)*(fx-fv);    if popbased==1 varevsij(,popbased)
       q=(x-v)*(fx-fw);    total life expectancies
       p=(x-v)*q-(x-w)*r;    Variance of period (stable) prevalence
       q=2.0*(q-r);   end
       if (q > 0.0) p = -p;  */
       q=fabs(q);  
       etemp=e;  
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))   
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  #include <math.h>
       else {  #include <stdio.h>
         d=p/q;  #include <stdlib.h>
         u=x+d;  #include <string.h>
         if (u-a < tol2 || b-u < tol2)  #include <unistd.h>
           d=SIGN(tol1,xm-x);  
       }  #include <limits.h>
     } else {  #include <sys/types.h>
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  #include <sys/stat.h>
     }  #include <errno.h>
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  extern int errno;
     fu=(*f)(u);  
     if (fu <= fx) {  #ifdef LINUX
       if (u >= x) a=x; else b=x;  #include <time.h>
       SHFT(v,w,x,u)  #include "timeval.h"
         SHFT(fv,fw,fx,fu)  #else
         } else {  #include <sys/time.h>
           if (u < x) a=u; else b=u;  #endif
           if (fu <= fw || w == x) {  
             v=w;  #ifdef GSL
             w=u;  #include <gsl/gsl_errno.h>
             fv=fw;  #include <gsl/gsl_multimin.h>
             fw=fu;  #endif
           } else if (fu <= fv || v == x || v == w) {  
             v=u;  /* #include <libintl.h> */
             fv=fu;  /* #define _(String) gettext (String) */
           }  
         }  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   }  
   nrerror("Too many iterations in brent");  #define GNUPLOTPROGRAM "gnuplot"
   *xmin=x;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   return fx;  #define FILENAMELENGTH 132
 }  
   #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 /****************** mnbrak ***********************/  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
             double (*func)(double))  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
 {  
   double ulim,u,r,q, dum;  #define NINTERVMAX 8
   double fu;  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
    #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
   *fa=(*func)(*ax);  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
   *fb=(*func)(*bx);  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
   if (*fb > *fa) {  #define MAXN 20000
     SHFT(dum,*ax,*bx,dum)  #define YEARM 12. /**< Number of months per year */
       SHFT(dum,*fb,*fa,dum)  #define AGESUP 130
       }  #define AGEBASE 40
   *cx=(*bx)+GOLD*(*bx-*ax);  #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
   *fc=(*func)(*cx);  #ifdef UNIX
   while (*fb > *fc) {  #define DIRSEPARATOR '/'
     r=(*bx-*ax)*(*fb-*fc);  #define CHARSEPARATOR "/"
     q=(*bx-*cx)*(*fb-*fa);  #define ODIRSEPARATOR '\\'
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  #else
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  #define DIRSEPARATOR '\\'
     ulim=(*bx)+GLIMIT*(*cx-*bx);  #define CHARSEPARATOR "\\"
     if ((*bx-u)*(u-*cx) > 0.0) {  #define ODIRSEPARATOR '/'
       fu=(*func)(u);  #endif
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  /* $Id$ */
       if (fu < *fc) {  /* $State$ */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  char version[]="Imach version 0.98nT, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
           }  char fullversion[]="$Revision$ $Date$"; 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  char strstart[80];
       u=ulim;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
       fu=(*func)(u);  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     } else {  int nvar=0, nforce=0; /* Number of variables, number of forces */
       u=(*cx)+GOLD*(*cx-*bx);  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
       fu=(*func)(u);  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
     }  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
     SHFT(*ax,*bx,*cx,u)  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
       SHFT(*fa,*fb,*fc,fu)  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
       }  int cptcovprodnoage=0; /**< Number of covariate products without age */   
 }  int cptcoveff=0; /* Total number of covariates to vary for printing results */
   int cptcov=0; /* Working variable */
 /*************** linmin ************************/  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
 int ncom;  int ndeath=1; /* Number of dead states */
 double *pcom,*xicom;  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 double (*nrfunc)(double []);  int popbased=0;
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  int *wav; /* Number of waves for this individuual 0 is possible */
 {  int maxwav=0; /* Maxim number of waves */
   double brent(double ax, double bx, double cx,  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
                double (*f)(double), double tol, double *xmin);  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
   double f1dim(double x);  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,                     to the likelihood and the sum of weights (done by funcone)*/
               double *fc, double (*func)(double));  int mle=1, weightopt=0;
   int j;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   double xx,xmin,bx,ax;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   double fx,fb,fa;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
               * wave mi and wave mi+1 is not an exact multiple of stepm. */
   ncom=n;  double jmean=1; /* Mean space between 2 waves */
   pcom=vector(1,n);  double **matprod2(); /* test */
   xicom=vector(1,n);  double **oldm, **newm, **savm; /* Working pointers to matrices */
   nrfunc=func;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   for (j=1;j<=n;j++) {  /*FILE *fic ; */ /* Used in readdata only */
     pcom[j]=p[j];  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
     xicom[j]=xi[j];  FILE *ficlog, *ficrespow;
   }  int globpr=0; /* Global variable for printing or not */
   ax=0.0;  double fretone; /* Only one call to likelihood */
   xx=1.0;  long ipmx=0; /* Number of contributions */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  double sw; /* Sum of weights */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  char filerespow[FILENAMELENGTH];
 #ifdef DEBUG  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  FILE *ficresilk;
 #endif  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   for (j=1;j<=n;j++) {  FILE *ficresprobmorprev;
     xi[j] *= xmin;  FILE *fichtm, *fichtmcov; /* Html File */
     p[j] += xi[j];  FILE *ficreseij;
   }  char filerese[FILENAMELENGTH];
   free_vector(xicom,1,n);  FILE *ficresstdeij;
   free_vector(pcom,1,n);  char fileresstde[FILENAMELENGTH];
 }  FILE *ficrescveij;
   char filerescve[FILENAMELENGTH];
 /*************** powell ************************/  FILE  *ficresvij;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  char fileresv[FILENAMELENGTH];
             double (*func)(double []))  FILE  *ficresvpl;
 {  char fileresvpl[FILENAMELENGTH];
   void linmin(double p[], double xi[], int n, double *fret,  char title[MAXLINE];
               double (*func)(double []));  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   int i,ibig,j;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   double del,t,*pt,*ptt,*xit;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   double fp,fptt;  char command[FILENAMELENGTH];
   double *xits;  int  outcmd=0;
   pt=vector(1,n);  
   ptt=vector(1,n);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   xit=vector(1,n);  
   xits=vector(1,n);  char filelog[FILENAMELENGTH]; /* Log file */
   *fret=(*func)(p);  char filerest[FILENAMELENGTH];
   for (j=1;j<=n;j++) pt[j]=p[j];  char fileregp[FILENAMELENGTH];
   for (*iter=1;;++(*iter)) {  char popfile[FILENAMELENGTH];
     fp=(*fret);  
     ibig=0;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     del=0.0;  
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
     for (i=1;i<=n;i++)  struct timezone tzp;
       printf(" %d %.12f",i, p[i]);  extern int gettimeofday();
     printf("\n");  struct tm tmg, tm, tmf, *gmtime(), *localtime();
     for (i=1;i<=n;i++) {  long time_value;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  extern long time();
       fptt=(*fret);  char strcurr[80], strfor[80];
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);  char *endptr;
 #endif  long lval;
       printf("%d",i);fflush(stdout);  double dval;
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {  #define NR_END 1
         del=fabs(fptt-(*fret));  #define FREE_ARG char*
         ibig=i;  #define FTOL 1.0e-10
       }  
 #ifdef DEBUG  #define NRANSI 
       printf("%d %.12e",i,(*fret));  #define ITMAX 200 
       for (j=1;j<=n;j++) {  
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  #define TOL 2.0e-4 
         printf(" x(%d)=%.12e",j,xit[j]);  
       }  #define CGOLD 0.3819660 
       for(j=1;j<=n;j++)  #define ZEPS 1.0e-10 
         printf(" p=%.12e",p[j]);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       printf("\n");  
 #endif  #define GOLD 1.618034 
     }  #define GLIMIT 100.0 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  #define TINY 1.0e-20 
 #ifdef DEBUG  
       int k[2],l;  static double maxarg1,maxarg2;
       k[0]=1;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       k[1]=-1;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       printf("Max: %.12e",(*func)(p));    
       for (j=1;j<=n;j++)  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
         printf(" %.12e",p[j]);  #define rint(a) floor(a+0.5)
       printf("\n");  
       for(l=0;l<=1;l++) {  static double sqrarg;
         for (j=1;j<=n;j++) {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  int agegomp= AGEGOMP;
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  int imx; 
       }  int stepm=1;
 #endif  /* Stepm, step in month: minimum step interpolation*/
   
   int estepm;
       free_vector(xit,1,n);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);  int m,nb;
       free_vector(pt,1,n);  long *num;
       return;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
     }  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  double **pmmij, ***probs;
     for (j=1;j<=n;j++) {  double *ageexmed,*agecens;
       ptt[j]=2.0*p[j]-pt[j];  double dateintmean=0;
       xit[j]=p[j]-pt[j];  
       pt[j]=p[j];  double *weight;
     }  int **s; /* Status */
     fptt=(*func)(ptt);  double *agedc;
     if (fptt < fp) {  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);                    * covar=matrix(0,NCOVMAX,1,n); 
       if (t < 0.0) {                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
         linmin(p,xit,n,fret,func);  double  idx; 
         for (j=1;j<=n;j++) {  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
           xi[j][ibig]=xi[j][n];  int *Ndum; /** Freq of modality (tricode */
           xi[j][n]=xit[j];  int **codtab; /**< codtab=imatrix(1,100,1,10); */
         }  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
 #ifdef DEBUG  double *lsurv, *lpop, *tpop;
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  
         for(j=1;j<=n;j++)  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
           printf(" %.12e",xit[j]);  double ftolhess; /**< Tolerance for computing hessian */
         printf("\n");  
 #endif  /**************** split *************************/
       }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     }  {
   }    /* 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)
     */ 
 /**** Prevalence limit ****************/    char  *ss;                            /* pointer */
     int   l1, l2;                         /* length counters */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  
 {    l1 = strlen(path );                   /* length of path */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
      matrix by transitions matrix until convergence is reached */    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so determine current directory */
   int i, ii,j,k;      strcpy( name, path );               /* we got the fullname name because no directory */
   double min, max, maxmin, maxmax,sumnew=0.;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   double **matprod2();        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   double **out, cov[NCOVMAX], **pmij();      /* get current working directory */
   double **newm;      /*    extern  char* getcwd ( char *buf , int len);*/
   double agefin, delaymax=50 ; /* Max number of years to converge */      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         return( GLOCK_ERROR_GETCWD );
   for (ii=1;ii<=nlstate+ndeath;ii++)      }
     for (j=1;j<=nlstate+ndeath;j++){      /* got dirc from getcwd*/
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      printf(" DIRC = %s \n",dirc);
     }    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
    cov[1]=1.;      l2 = strlen( ss );                  /* length of filename */
        if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      strcpy( name, ss );         /* save file name */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     newm=savm;      dirc[l1-l2] = 0;                    /* add zero */
     /* Covariates have to be included here again */      printf(" DIRC2 = %s \n",dirc);
      cov[2]=agefin;    }
      /* We add a separator at the end of dirc if not exists */
       for (k=1; k<=cptcovn;k++) {    l1 = strlen( dirc );                  /* length of directory */
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    if( dirc[l1-1] != DIRSEPARATOR ){
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/      dirc[l1] =  DIRSEPARATOR;
       }      dirc[l1+1] = 0; 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      printf(" DIRC3 = %s \n",dirc);
       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]]];    ss = strrchr( name, '.' );            /* find last / */
     if (ss >0){
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      ss++;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      strcpy(ext,ss);                     /* save extension */
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      l1= strlen( name);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      l2= strlen(ss)+1;
       strncpy( finame, name, l1-l2);
     savm=oldm;      finame[l1-l2]= 0;
     oldm=newm;    }
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){    return( 0 );                          /* we're done */
       min=1.;  }
       max=0.;  
       for(i=1; i<=nlstate; i++) {  
         sumnew=0;  /******************************************/
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  void replace_back_to_slash(char *s, char*t)
         max=FMAX(max,prlim[i][j]);  {
         min=FMIN(min,prlim[i][j]);    int i;
       }    int lg=0;
       maxmin=max-min;    i=0;
       maxmax=FMAX(maxmax,maxmin);    lg=strlen(t);
     }    for(i=0; i<= lg; i++) {
     if(maxmax < ftolpl){      (s[i] = t[i]);
       return prlim;      if (t[i]== '\\') s[i]='/';
     }    }
   }  }
 }  
   char *trimbb(char *out, char *in)
 /*************** transition probabilities ***************/  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
     char *s;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    s=out;
 {    while (*in != '\0'){
   double s1, s2;      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
   /*double t34;*/        in++;
   int i,j,j1, nc, ii, jj;      }
       *out++ = *in++;
     for(i=1; i<= nlstate; i++){    }
     for(j=1; j<i;j++){    *out='\0';
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    return s;
         /*s2 += param[i][j][nc]*cov[nc];*/  }
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  char *cutl(char *blocc, char *alocc, char *in, char occ)
       }  {
       ps[i][j]=s2;    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
     }       gives blocc="abcdef2ghi" and alocc="j".
     for(j=i+1; j<=nlstate+ndeath;j++){       If occ is not found blocc is null and alocc is equal to in. Returns blocc
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    */
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    char *s, *t, *bl;
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    t=in;s=in;
       }    while ((*in != occ) && (*in != '\0')){
       ps[i][j]=s2;      *alocc++ = *in++;
     }    }
   }    if( *in == occ){
     /*ps[3][2]=1;*/      *(alocc)='\0';
       s=++in;
   for(i=1; i<= nlstate; i++){    }
      s1=0;   
     for(j=1; j<i; j++)    if (s == t) {/* occ not found */
       s1+=exp(ps[i][j]);      *(alocc-(in-s))='\0';
     for(j=i+1; j<=nlstate+ndeath; j++)      in=s;
       s1+=exp(ps[i][j]);    }
     ps[i][i]=1./(s1+1.);    while ( *in != '\0'){
     for(j=1; j<i; j++)      *blocc++ = *in++;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    }
     for(j=i+1; j<=nlstate+ndeath; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];    *blocc='\0';
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    return t;
   } /* end i */  }
   char *cutv(char *blocc, char *alocc, char *in, char occ)
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  {
     for(jj=1; jj<= nlstate+ndeath; jj++){    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
       ps[ii][jj]=0;       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
       ps[ii][ii]=1;       gives blocc="abcdef2ghi" and alocc="j".
     }       If occ is not found blocc is null and alocc is equal to in. Returns alocc
   }    */
     char *s, *t;
     t=in;s=in;
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    while (*in != '\0'){
     for(jj=1; jj<= nlstate+ndeath; jj++){      while( *in == occ){
      printf("%lf ",ps[ii][jj]);        *blocc++ = *in++;
    }        s=in;
     printf("\n ");      }
     }      *blocc++ = *in++;
     printf("\n ");printf("%lf ",cov[2]);*/    }
 /*    if (s == t) /* occ not found */
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      *(blocc-(in-s))='\0';
   goto end;*/    else
     return ps;      *(blocc-(in-s)-1)='\0';
 }    in=s;
     while ( *in != '\0'){
 /**************** Product of 2 matrices ******************/      *alocc++ = *in++;
     }
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  
 {    *alocc='\0';
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    return s;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  }
   /* in, b, out are matrice of pointers which should have been initialized  
      before: only the contents of out is modified. The function returns  int nbocc(char *s, char occ)
      a pointer to pointers identical to out */  {
   long i, j, k;    int i,j=0;
   for(i=nrl; i<= nrh; i++)    int lg=20;
     for(k=ncolol; k<=ncoloh; k++)    i=0;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    lg=strlen(s);
         out[i][k] +=in[i][j]*b[j][k];    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
   return out;    }
 }    return j;
   }
   
 /************* Higher Matrix Product ***************/  /* void cutv(char *u,char *v, char*t, char occ) */
   /* { */
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
 {  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  /*      gives u="abcdef2ghi" and v="j" *\/ */
      duration (i.e. until  /*   int i,lg,j,p=0; */
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  /*   i=0; */
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  /*   lg=strlen(t); */
      (typically every 2 years instead of every month which is too big).  /*   for(j=0; j<=lg-1; j++) { */
      Model is determined by parameters x and covariates have to be  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
      included manually here.  /*   } */
   
      */  /*   for(j=0; j<p; j++) { */
   /*     (u[j] = t[j]); */
   int i, j, d, h, k;  /*   } */
   double **out, cov[NCOVMAX];  /*      u[p]='\0'; */
   double **newm;  
   /*    for(j=0; j<= lg; j++) { */
   /* Hstepm could be zero and should return the unit matrix */  /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   for (i=1;i<=nlstate+ndeath;i++)  /*   } */
     for (j=1;j<=nlstate+ndeath;j++){  /* } */
       oldm[i][j]=(i==j ? 1.0 : 0.0);  
       po[i][j][0]=(i==j ? 1.0 : 0.0);  /********************** nrerror ********************/
     }  
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  void nrerror(char error_text[])
   for(h=1; h <=nhstepm; h++){  {
     for(d=1; d <=hstepm; d++){    fprintf(stderr,"ERREUR ...\n");
       newm=savm;    fprintf(stderr,"%s\n",error_text);
       /* Covariates have to be included here again */    exit(EXIT_FAILURE);
       cov[1]=1.;  }
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  /*********************** vector *******************/
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  double *vector(int nl, int nh)
       for (k=1; k<=cptcovage;k++)  {
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    double *v;
       for (k=1; k<=cptcovprod;k++)    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
   }
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  /************************ free vector ******************/
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  void free_vector(double*v, int nl, int nh)
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  {
       savm=oldm;    free((FREE_ARG)(v+nl-NR_END));
       oldm=newm;  }
     }  
     for(i=1; i<=nlstate+ndeath; i++)  /************************ivector *******************************/
       for(j=1;j<=nlstate+ndeath;j++) {  int *ivector(long nl,long nh)
         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]);    int *v;
          */    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       }    if (!v) nrerror("allocation failure in ivector");
   } /* end h */    return v-nl+NR_END;
   return po;  }
 }  
   /******************free ivector **************************/
   void free_ivector(int *v, long nl, long nh)
 /*************** log-likelihood *************/  {
 double func( double *x)    free((FREE_ARG)(v+nl-NR_END));
 {  }
   int i, ii, j, k, mi, d, kk;  
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  /************************lvector *******************************/
   double **out;  long *lvector(long nl,long nh)
   double sw; /* Sum of weights */  {
   double lli; /* Individual log likelihood */    long *v;
   long ipmx;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   /*extern weight */    if (!v) nrerror("allocation failure in ivector");
   /* We are differentiating ll according to initial status */    return v-nl+NR_END;
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  }
   /*for(i=1;i<imx;i++)  
     printf(" %d\n",s[4][i]);  /******************free lvector **************************/
   */  void free_lvector(long *v, long nl, long nh)
   cov[1]=1.;  {
     free((FREE_ARG)(v+nl-NR_END));
   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];  /******************* imatrix *******************************/
     for(mi=1; mi<= wav[i]-1; mi++){  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       for (ii=1;ii<=nlstate+ndeath;ii++)       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  { 
       for(d=0; d<dh[mi][i]; d++){    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
         newm=savm;    int **m; 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    
         for (kk=1; kk<=cptcovage;kk++) {    /* allocate pointers to rows */ 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         }    if (!m) nrerror("allocation failure 1 in matrix()"); 
            m += NR_END; 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    m -= nrl; 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    
         savm=oldm;    
         oldm=newm;    /* allocate rows and set pointers to them */ 
            m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
            if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       } /* end mult */    m[nrl] += NR_END; 
          m[nrl] -= ncl; 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       ipmx +=1;    
       sw += weight[i];    /* return pointer to array of pointers to rows */ 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    return m; 
     } /* end of wave */  } 
   } /* end of individual */  
   /****************** free_imatrix *************************/
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  void free_imatrix(m,nrl,nrh,ncl,nch)
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        int **m;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        long nch,ncl,nrh,nrl; 
   return -l;       /* free an int matrix allocated by imatrix() */ 
 }  { 
     free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     free((FREE_ARG) (m+nrl-NR_END)); 
 /*********** Maximum Likelihood Estimation ***************/  } 
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  /******************* matrix *******************************/
 {  double **matrix(long nrl, long nrh, long ncl, long nch)
   int i,j, iter;  {
   double **xi,*delti;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   double fret;    double **m;
   xi=matrix(1,npar,1,npar);  
   for (i=1;i<=npar;i++)    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     for (j=1;j<=npar;j++)    if (!m) nrerror("allocation failure 1 in matrix()");
       xi[i][j]=(i==j ? 1.0 : 0.0);    m += NR_END;
   printf("Powell\n");    m -= nrl;
   powell(p,xi,npar,ftol,&iter,&fret,func);  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    m[nrl] += NR_END;
     m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 /**** Computes Hessian and covariance matrix ***/    return m;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
 {  m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
   double  **a,**y,*x,pd;  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
   double **hess;     */
   int i, j,jk;  }
   int *indx;  
   /*************************free matrix ************************/
   double hessii(double p[], double delta, int theta, double delti[]);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double hessij(double p[], double delti[], int i, int j);  {
   void lubksb(double **a, int npar, int *indx, double b[]) ;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   void ludcmp(double **a, int npar, int *indx, double *d) ;    free((FREE_ARG)(m+nrl-NR_END));
   }
   hess=matrix(1,npar,1,npar);  
   /******************* ma3x *******************************/
   printf("\nCalculation of the hessian matrix. Wait...\n");  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   for (i=1;i<=npar;i++){  {
     printf("%d",i);fflush(stdout);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     hess[i][i]=hessii(p,ftolhess,i,delti);    double ***m;
     /*printf(" %f ",p[i]);*/  
     /*printf(" %lf ",hess[i][i]);*/    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   }    if (!m) nrerror("allocation failure 1 in matrix()");
      m += NR_END;
   for (i=1;i<=npar;i++) {    m -= nrl;
     for (j=1;j<=npar;j++)  {  
       if (j>i) {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         printf(".%d%d",i,j);fflush(stdout);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         hess[i][j]=hessij(p,delti,i,j);    m[nrl] += NR_END;
         hess[j][i]=hess[i][j];        m[nrl] -= ncl;
         /*printf(" %lf ",hess[i][j]);*/  
       }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     }  
   }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   printf("\n");    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     m[nrl][ncl] += NR_END;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    m[nrl][ncl] -= nll;
      for (j=ncl+1; j<=nch; j++) 
   a=matrix(1,npar,1,npar);      m[nrl][j]=m[nrl][j-1]+nlay;
   y=matrix(1,npar,1,npar);    
   x=vector(1,npar);    for (i=nrl+1; i<=nrh; i++) {
   indx=ivector(1,npar);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   for (i=1;i<=npar;i++)      for (j=ncl+1; j<=nch; j++) 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        m[i][j]=m[i][j-1]+nlay;
   ludcmp(a,npar,indx,&pd);    }
     return m; 
   for (j=1;j<=npar;j++) {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     for (i=1;i<=npar;i++) x[i]=0;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     x[j]=1;    */
     lubksb(a,npar,indx,x);  }
     for (i=1;i<=npar;i++){  
       matcov[i][j]=x[i];  /*************************free ma3x ************************/
     }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   }  {
     free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   printf("\n#Hessian matrix#\n");    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   for (i=1;i<=npar;i++) {    free((FREE_ARG)(m+nrl-NR_END));
     for (j=1;j<=npar;j++) {  }
       printf("%.3e ",hess[i][j]);  
     }  /*************** function subdirf ***********/
     printf("\n");  char *subdirf(char fileres[])
   }  {
     /* Caution optionfilefiname is hidden */
   /* Recompute Inverse */    strcpy(tmpout,optionfilefiname);
   for (i=1;i<=npar;i++)    strcat(tmpout,"/"); /* Add to the right */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    strcat(tmpout,fileres);
   ludcmp(a,npar,indx,&pd);    return tmpout;
   }
   /*  printf("\n#Hessian matrix recomputed#\n");  
   /*************** function subdirf2 ***********/
   for (j=1;j<=npar;j++) {  char *subdirf2(char fileres[], char *preop)
     for (i=1;i<=npar;i++) x[i]=0;  {
     x[j]=1;    
     lubksb(a,npar,indx,x);    /* Caution optionfilefiname is hidden */
     for (i=1;i<=npar;i++){    strcpy(tmpout,optionfilefiname);
       y[i][j]=x[i];    strcat(tmpout,"/");
       printf("%.3e ",y[i][j]);    strcat(tmpout,preop);
     }    strcat(tmpout,fileres);
     printf("\n");    return tmpout;
   }  }
   */  
   /*************** function subdirf3 ***********/
   free_matrix(a,1,npar,1,npar);  char *subdirf3(char fileres[], char *preop, char *preop2)
   free_matrix(y,1,npar,1,npar);  {
   free_vector(x,1,npar);    
   free_ivector(indx,1,npar);    /* Caution optionfilefiname is hidden */
   free_matrix(hess,1,npar,1,npar);    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
     strcat(tmpout,preop);
 }    strcat(tmpout,preop2);
     strcat(tmpout,fileres);
 /*************** hessian matrix ****************/    return tmpout;
 double hessii( double x[], double delta, int theta, double delti[])  }
 {  
   int i;  /***************** f1dim *************************/
   int l=1, lmax=20;  extern int ncom; 
   double k1,k2;  extern double *pcom,*xicom;
   double p2[NPARMAX+1];  extern double (*nrfunc)(double []); 
   double res;   
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  double f1dim(double x) 
   double fx;  { 
   int k=0,kmax=10;    int j; 
   double l1;    double f;
     double *xt; 
   fx=func(x);   
   for (i=1;i<=npar;i++) p2[i]=x[i];    xt=vector(1,ncom); 
   for(l=0 ; l <=lmax; l++){    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     l1=pow(10,l);    f=(*nrfunc)(xt); 
     delts=delt;    free_vector(xt,1,ncom); 
     for(k=1 ; k <kmax; k=k+1){    return f; 
       delt = delta*(l1*k);  } 
       p2[theta]=x[theta] +delt;  
       k1=func(p2)-fx;  /*****************brent *************************/
       p2[theta]=x[theta]-delt;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       k2=func(p2)-fx;  { 
       /*res= (k1-2.0*fx+k2)/delt/delt; */    int iter; 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    double a,b,d,etemp;
          double fu,fv,fw,fx;
 #ifdef DEBUG    double ftemp;
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
 #endif    double e=0.0; 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */   
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    a=(ax < cx ? ax : cx); 
         k=kmax;    b=(ax > cx ? ax : cx); 
       }    x=w=v=bx; 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    fw=fv=fx=(*f)(x); 
         k=kmax; l=lmax*10.;    for (iter=1;iter<=ITMAX;iter++) { 
       }      xm=0.5*(a+b); 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         delts=delt;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       }      printf(".");fflush(stdout);
     }      fprintf(ficlog,".");fflush(ficlog);
   }  #ifdef DEBUG
   delti[theta]=delts;      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   return res;      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
        /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 }  #endif
       if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 double hessij( double x[], double delti[], int thetai,int thetaj)        *xmin=x; 
 {        return fx; 
   int i;      } 
   int l=1, l1, lmax=20;      ftemp=fu;
   double k1,k2,k3,k4,res,fx;      if (fabs(e) > tol1) { 
   double p2[NPARMAX+1];        r=(x-w)*(fx-fv); 
   int k;        q=(x-v)*(fx-fw); 
         p=(x-v)*q-(x-w)*r; 
   fx=func(x);        q=2.0*(q-r); 
   for (k=1; k<=2; k++) {        if (q > 0.0) p = -p; 
     for (i=1;i<=npar;i++) p2[i]=x[i];        q=fabs(q); 
     p2[thetai]=x[thetai]+delti[thetai]/k;        etemp=e; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        e=d; 
     k1=func(p2)-fx;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
            d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     p2[thetai]=x[thetai]+delti[thetai]/k;        else { 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          d=p/q; 
     k2=func(p2)-fx;          u=x+d; 
            if (u-a < tol2 || b-u < tol2) 
     p2[thetai]=x[thetai]-delti[thetai]/k;            d=SIGN(tol1,xm-x); 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        } 
     k3=func(p2)-fx;      } else { 
          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     p2[thetai]=x[thetai]-delti[thetai]/k;      } 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     k4=func(p2)-fx;      fu=(*f)(u); 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      if (fu <= fx) { 
 #ifdef DEBUG        if (u >= x) a=x; else b=x; 
     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);        SHFT(v,w,x,u) 
 #endif          SHFT(fv,fw,fx,fu) 
   }          } else { 
   return res;            if (u < x) a=u; else b=u; 
 }            if (fu <= fw || w == x) { 
               v=w; 
 /************** Inverse of matrix **************/              w=u; 
 void ludcmp(double **a, int n, int *indx, double *d)              fv=fw; 
 {              fw=fu; 
   int i,imax,j,k;            } else if (fu <= fv || v == x || v == w) { 
   double big,dum,sum,temp;              v=u; 
   double *vv;              fv=fu; 
              } 
   vv=vector(1,n);          } 
   *d=1.0;    } 
   for (i=1;i<=n;i++) {    nrerror("Too many iterations in brent"); 
     big=0.0;    *xmin=x; 
     for (j=1;j<=n;j++)    return fx; 
       if ((temp=fabs(a[i][j])) > big) big=temp;  } 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  
     vv[i]=1.0/big;  /****************** mnbrak ***********************/
   }  
   for (j=1;j<=n;j++) {  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     for (i=1;i<j;i++) {              double (*func)(double)) 
       sum=a[i][j];  { 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    double ulim,u,r,q, dum;
       a[i][j]=sum;    double fu; 
     }   
     big=0.0;    *fa=(*func)(*ax); 
     for (i=j;i<=n;i++) {    *fb=(*func)(*bx); 
       sum=a[i][j];    if (*fb > *fa) { 
       for (k=1;k<j;k++)      SHFT(dum,*ax,*bx,dum) 
         sum -= a[i][k]*a[k][j];        SHFT(dum,*fb,*fa,dum) 
       a[i][j]=sum;        } 
       if ( (dum=vv[i]*fabs(sum)) >= big) {    *cx=(*bx)+GOLD*(*bx-*ax); 
         big=dum;    *fc=(*func)(*cx); 
         imax=i;    while (*fb > *fc) { 
       }      r=(*bx-*ax)*(*fb-*fc); 
     }      q=(*bx-*cx)*(*fb-*fa); 
     if (j != imax) {      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       for (k=1;k<=n;k++) {        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
         dum=a[imax][k];      ulim=(*bx)+GLIMIT*(*cx-*bx); 
         a[imax][k]=a[j][k];      if ((*bx-u)*(u-*cx) > 0.0) { 
         a[j][k]=dum;        fu=(*func)(u); 
       }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       *d = -(*d);        fu=(*func)(u); 
       vv[imax]=vv[j];        if (fu < *fc) { 
     }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     indx[j]=imax;            SHFT(*fb,*fc,fu,(*func)(u)) 
     if (a[j][j] == 0.0) a[j][j]=TINY;            } 
     if (j != n) {      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       dum=1.0/(a[j][j]);        u=ulim; 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        fu=(*func)(u); 
     }      } else { 
   }        u=(*cx)+GOLD*(*cx-*bx); 
   free_vector(vv,1,n);  /* Doesn't work */        fu=(*func)(u); 
 ;      } 
 }      SHFT(*ax,*bx,*cx,u) 
         SHFT(*fa,*fb,*fc,fu) 
 void lubksb(double **a, int n, int *indx, double b[])        } 
 {  } 
   int i,ii=0,ip,j;  
   double sum;  /*************** linmin ************************/
    
   for (i=1;i<=n;i++) {  int ncom; 
     ip=indx[i];  double *pcom,*xicom;
     sum=b[ip];  double (*nrfunc)(double []); 
     b[ip]=b[i];   
     if (ii)  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  { 
     else if (sum) ii=i;    double brent(double ax, double bx, double cx, 
     b[i]=sum;                 double (*f)(double), double tol, double *xmin); 
   }    double f1dim(double x); 
   for (i=n;i>=1;i--) {    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     sum=b[i];                double *fc, double (*func)(double)); 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    int j; 
     b[i]=sum/a[i][i];    double xx,xmin,bx,ax; 
   }    double fx,fb,fa;
 }   
     ncom=n; 
 /************ Frequencies ********************/    pcom=vector(1,n); 
 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)    xicom=vector(1,n); 
 {  /* Some frequencies */    nrfunc=func; 
      for (j=1;j<=n;j++) { 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;      pcom[j]=p[j]; 
   double ***freq; /* Frequencies */      xicom[j]=xi[j]; 
   double *pp;    } 
   double pos, k2, dateintsum=0,k2cpt=0;    ax=0.0; 
   FILE *ficresp;    xx=1.0; 
   char fileresp[FILENAMELENGTH];    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
      *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   pp=vector(1,nlstate);  #ifdef DEBUG
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   strcpy(fileresp,"p");    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   strcat(fileresp,fileres);  #endif
   if((ficresp=fopen(fileresp,"w"))==NULL) {    for (j=1;j<=n;j++) { 
     printf("Problem with prevalence resultfile: %s\n", fileresp);      xi[j] *= xmin; 
     exit(0);      p[j] += xi[j]; 
   }    } 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    free_vector(xicom,1,n); 
   j1=0;    free_vector(pcom,1,n); 
    } 
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  char *asc_diff_time(long time_sec, char ascdiff[])
    {
   for(k1=1; k1<=j;k1++){    long sec_left, days, hours, minutes;
     for(i1=1; i1<=ncodemax[k1];i1++){    days = (time_sec) / (60*60*24);
       j1++;    sec_left = (time_sec) % (60*60*24);
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    hours = (sec_left) / (60*60) ;
         scanf("%d", i);*/    sec_left = (sec_left) %(60*60);
       for (i=-1; i<=nlstate+ndeath; i++)      minutes = (sec_left) /60;
         for (jk=-1; jk<=nlstate+ndeath; jk++)      sec_left = (sec_left) % (60);
           for(m=agemin; m <= agemax+3; m++)    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
             freq[i][jk][m]=0;    return ascdiff;
        }
       dateintsum=0;  
       k2cpt=0;  /*************** powell ************************/
       for (i=1; i<=imx; i++) {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         bool=1;              double (*func)(double [])) 
         if  (cptcovn>0) {  { 
           for (z1=1; z1<=cptcoveff; z1++)    void linmin(double p[], double xi[], int n, double *fret, 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])                double (*func)(double [])); 
               bool=0;    int i,ibig,j; 
         }    double del,t,*pt,*ptt,*xit;
         if (bool==1) {    double fp,fptt;
           for(m=firstpass; m<=lastpass; m++){    double *xits;
             k2=anint[m][i]+(mint[m][i]/12.);    int niterf, itmp;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  
               if(agev[m][i]==0) agev[m][i]=agemax+1;    pt=vector(1,n); 
               if(agev[m][i]==1) agev[m][i]=agemax+2;    ptt=vector(1,n); 
               if (m<lastpass) {    xit=vector(1,n); 
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    xits=vector(1,n); 
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];    *fret=(*func)(p); 
               }    for (j=1;j<=n;j++) pt[j]=p[j]; 
                  for (*iter=1;;++(*iter)) { 
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {      fp=(*fret); 
                 dateintsum=dateintsum+k2;      ibig=0; 
                 k2cpt++;      del=0.0; 
               }      last_time=curr_time;
             }      (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);
         }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
       }  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
             for (i=1;i<=n;i++) {
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        printf(" %d %.12f",i, p[i]);
         fprintf(ficlog," %d %.12lf",i, p[i]);
       if  (cptcovn>0) {        fprintf(ficrespow," %.12lf", p[i]);
         fprintf(ficresp, "\n#********** Variable ");      }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      printf("\n");
         fprintf(ficresp, "**********\n#");      fprintf(ficlog,"\n");
       }      fprintf(ficrespow,"\n");fflush(ficrespow);
       for(i=1; i<=nlstate;i++)      if(*iter <=3){
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        tm = *localtime(&curr_time.tv_sec);
       fprintf(ficresp, "\n");        strcpy(strcurr,asctime(&tm));
        /*       asctime_r(&tm,strcurr); */
       for(i=(int)agemin; i <= (int)agemax+3; i++){        forecast_time=curr_time; 
         if(i==(int)agemax+3)        itmp = strlen(strcurr);
           printf("Total");        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
         else          strcurr[itmp-1]='\0';
           printf("Age %d", i);        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         for(jk=1; jk <=nlstate ; jk++){        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        for(niterf=10;niterf<=30;niterf+=10){
             pp[jk] += freq[jk][m][i];          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
         }          tmf = *localtime(&forecast_time.tv_sec);
         for(jk=1; jk <=nlstate ; jk++){  /*      asctime_r(&tmf,strfor); */
           for(m=-1, pos=0; m <=0 ; m++)          strcpy(strfor,asctime(&tmf));
             pos += freq[jk][m][i];          itmp = strlen(strfor);
           if(pp[jk]>=1.e-10)          if(strfor[itmp-1]=='\n')
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          strfor[itmp-1]='\0';
           else          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);
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          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);
         }        }
       }
         for(jk=1; jk <=nlstate ; jk++){      for (i=1;i<=n;i++) { 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
             pp[jk] += freq[jk][m][i];        fptt=(*fret); 
         }  #ifdef DEBUG
         printf("fret=%lf \n",*fret);
         for(jk=1,pos=0; jk <=nlstate ; jk++)        fprintf(ficlog,"fret=%lf \n",*fret);
           pos += pp[jk];  #endif
         for(jk=1; jk <=nlstate ; jk++){        printf("%d",i);fflush(stdout);
           if(pos>=1.e-5)        fprintf(ficlog,"%d",i);fflush(ficlog);
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        linmin(p,xit,n,fret,func); 
           else        if (fabs(fptt-(*fret)) > del) { 
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          del=fabs(fptt-(*fret)); 
           if( i <= (int) agemax){          ibig=i; 
             if(pos>=1.e-5){        } 
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  #ifdef DEBUG
               probs[i][jk][j1]= pp[jk]/pos;        printf("%d %.12e",i,(*fret));
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        fprintf(ficlog,"%d %.12e",i,(*fret));
             }        for (j=1;j<=n;j++) {
             else          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          printf(" x(%d)=%.12e",j,xit[j]);
           }          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }        }
                for(j=1;j<=n;j++) {
         for(jk=-1; jk <=nlstate+ndeath; jk++)          printf(" p=%.12e",p[j]);
           for(m=-1; m <=nlstate+ndeath; m++)          fprintf(ficlog," p=%.12e",p[j]);
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        }
         if(i <= (int) agemax)        printf("\n");
           fprintf(ficresp,"\n");        fprintf(ficlog,"\n");
         printf("\n");  #endif
       }      } 
     }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   }  #ifdef DEBUG
   dateintmean=dateintsum/k2cpt;        int k[2],l;
          k[0]=1;
   fclose(ficresp);        k[1]=-1;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        printf("Max: %.12e",(*func)(p));
   free_vector(pp,1,nlstate);        fprintf(ficlog,"Max: %.12e",(*func)(p));
          for (j=1;j<=n;j++) {
   /* End of Freq */          printf(" %.12e",p[j]);
 }          fprintf(ficlog," %.12e",p[j]);
         }
 /************ Prevalence ********************/        printf("\n");
 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)        fprintf(ficlog,"\n");
 {  /* Some frequencies */        for(l=0;l<=1;l++) {
            for (j=1;j<=n;j++) {
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   double ***freq; /* Frequencies */            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   double *pp;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   double pos, k2;          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   pp=vector(1,nlstate);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        }
    #endif
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  
   j1=0;  
          free_vector(xit,1,n); 
   j=cptcoveff;        free_vector(xits,1,n); 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        free_vector(ptt,1,n); 
          free_vector(pt,1,n); 
   for(k1=1; k1<=j;k1++){        return; 
     for(i1=1; i1<=ncodemax[k1];i1++){      } 
       j1++;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
            for (j=1;j<=n;j++) { 
       for (i=-1; i<=nlstate+ndeath; i++)          ptt[j]=2.0*p[j]-pt[j]; 
         for (jk=-1; jk<=nlstate+ndeath; jk++)          xit[j]=p[j]-pt[j]; 
           for(m=agemin; m <= agemax+3; m++)        pt[j]=p[j]; 
             freq[i][jk][m]=0;      } 
            fptt=(*func)(ptt); 
       for (i=1; i<=imx; i++) {      if (fptt < fp) { 
         bool=1;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         if  (cptcovn>0) {        if (t < 0.0) { 
           for (z1=1; z1<=cptcoveff; z1++)          linmin(p,xit,n,fret,func); 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          for (j=1;j<=n;j++) { 
               bool=0;            xi[j][ibig]=xi[j][n]; 
         }            xi[j][n]=xit[j]; 
         if (bool==1) {          }
           for(m=firstpass; m<=lastpass; m++){  #ifdef DEBUG
             k2=anint[m][i]+(mint[m][i]/12.);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
               if(agev[m][i]==0) agev[m][i]=agemax+1;          for(j=1;j<=n;j++){
               if(agev[m][i]==1) agev[m][i]=agemax+2;            printf(" %.12e",xit[j]);
               if (m<lastpass) {            fprintf(ficlog," %.12e",xit[j]);
                 if (calagedate>0)          }
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          printf("\n");
                 else          fprintf(ficlog,"\n");
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  #endif
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];        }
               }      } 
             }    } 
           }  } 
         }  
       }  /**** Prevalence limit (stable or period prevalence)  ****************/
       for(i=(int)agemin; i <= (int)agemax+3; i++){  
         for(jk=1; jk <=nlstate ; jk++){  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  {
             pp[jk] += freq[jk][m][i];    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         }       matrix by transitions matrix until convergence is reached */
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pos=0; m <=0 ; m++)    int i, ii,j,k;
             pos += freq[jk][m][i];    double min, max, maxmin, maxmax,sumnew=0.;
         }    /* double **matprod2(); */ /* test */
            double **out, cov[NCOVMAX+1], **pmij();
         for(jk=1; jk <=nlstate ; jk++){    double **newm;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    double agefin, delaymax=50 ; /* Max number of years to converge */
             pp[jk] += freq[jk][m][i];  
         }    for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
         for(jk=1; jk <=nlstate ; jk++){      
           if( i <= (int) agemax){     cov[1]=1.;
             if(pos>=1.e-5){   
               probs[i][jk][j1]= pp[jk]/pos;   /* 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 */
              cov[2]=agefin;
       }      
     }      for (k=1; k<=cptcovn;k++) {
   }        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         /*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]]);*/
        }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
   free_vector(pp,1,nlstate);      /* 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]]]; */
 }  /* End of Freq */      
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
 /************* Waves Concatenation ***************/      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
 {      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
      Death is a valid wave (if date is known).      
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      savm=oldm;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      oldm=newm;
      and mw[mi+1][i]. dh depends on stepm.      maxmax=0.;
      */      for(j=1;j<=nlstate;j++){
         min=1.;
   int i, mi, m;        max=0.;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        for(i=1; i<=nlstate; i++) {
      double sum=0., jmean=0.;*/          sumnew=0;
           for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   int j, k=0,jk, ju, jl;          prlim[i][j]= newm[i][j]/(1-sumnew);
   double sum=0.;          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
   jmin=1e+5;          max=FMAX(max,prlim[i][j]);
   jmax=-1;          min=FMIN(min,prlim[i][j]);
   jmean=0.;        }
   for(i=1; i<=imx; i++){        maxmin=max-min;
     mi=0;        maxmax=FMAX(maxmax,maxmin);
     m=firstpass;      }
     while(s[m][i] <= nlstate){      if(maxmax < ftolpl){
       if(s[m][i]>=1)        return prlim;
         mw[++mi][i]=m;      }
       if(m >=lastpass)    }
         break;  }
       else  
         m++;  /*************** transition probabilities ***************/ 
     }/* end while */  
     if (s[m][i] > nlstate){  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       mi++;     /* Death is another wave */  {
       /* if(mi==0)  never been interviewed correctly before death */    /* According to parameters values stored in x and the covariate's values stored in cov,
          /* Only death is a correct wave */       computes the probability to be observed in state j being in state i by appying the
       mw[mi][i]=m;       model to the ncovmodel covariates (including constant and age).
     }       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
        and, according on how parameters are entered, the position of the coefficient xij(nc) of the
     wav[i]=mi;       ncth covariate in the global vector x is given by the formula:
     if(mi==0)       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
   }       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
        sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
   for(i=1; i<=imx; i++){       Outputs ps[i][j] the probability to be observed in j being in j according to
     for(mi=1; mi<wav[i];mi++){       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
       if (stepm <=0)    */
         dh[mi][i]=1;    double s1, lnpijopii;
       else{    /*double t34;*/
         if (s[mw[mi+1][i]][i] > nlstate) {    int i,j,j1, nc, ii, jj;
           if (agedc[i] < 2*AGESUP) {  
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      for(i=1; i<= nlstate; i++){
           if(j==0) j=1;  /* Survives at least one month after exam */        for(j=1; j<i;j++){
           k=k+1;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
           if (j >= jmax) jmax=j;            /*lnpijopii += param[i][j][nc]*cov[nc];*/
           if (j <= jmin) jmin=j;            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
           sum=sum+j;  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
           /*if (j<0) printf("j=%d num=%d \n",j,i); */          }
           }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         }  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
         else{        }
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        for(j=i+1; j<=nlstate+ndeath;j++){
           k=k+1;          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
           if (j >= jmax) jmax=j;            /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
           else if (j <= jmin)jmin=j;            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
           sum=sum+j;          }
         }          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         jk= j/stepm;        }
         jl= j -jk*stepm;      }
         ju= j -(jk+1)*stepm;      
         if(jl <= -ju)      for(i=1; i<= nlstate; i++){
           dh[mi][i]=jk;        s1=0;
         else        for(j=1; j<i; j++){
           dh[mi][i]=jk+1;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
         if(dh[mi][i]==0)          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           dh[mi][i]=1; /* At least one step */        }
       }        for(j=i+1; j<=nlstate+ndeath; j++){
     }          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
   }          /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
   jmean=sum/k;        }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
  }        ps[i][i]=1./(s1+1.);
 /*********** Tricode ****************************/        /* Computing other pijs */
 void tricode(int *Tvar, int **nbcode, int imx)        for(j=1; j<i; j++)
 {          ps[i][j]= exp(ps[i][j])*ps[i][i];
   int Ndum[20],ij=1, k, j, i;        for(j=i+1; j<=nlstate+ndeath; j++)
   int cptcode=0;          ps[i][j]= exp(ps[i][j])*ps[i][i];
   cptcoveff=0;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
        } /* end i */
   for (k=0; k<19; k++) Ndum[k]=0;      
   for (k=1; k<=7; k++) ncodemax[k]=0;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         for(jj=1; jj<= nlstate+ndeath; jj++){
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          ps[ii][jj]=0;
     for (i=1; i<=imx; i++) {          ps[ii][ii]=1;
       ij=(int)(covar[Tvar[j]][i]);        }
       Ndum[ij]++;      }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      
       if (ij > cptcode) cptcode=ij;      
     }      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
       /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
     for (i=0; i<=cptcode; i++) {      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
       if(Ndum[i]!=0) ncodemax[j]++;      /*   } */
     }      /*   printf("\n "); */
     ij=1;      /* } */
       /* printf("\n ");printf("%lf ",cov[2]);*/
       /*
     for (i=1; i<=ncodemax[j]; i++) {        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       for (k=0; k<=19; k++) {        goto end;*/
         if (Ndum[k] != 0) {      return ps;
           nbcode[Tvar[j]][ij]=k;  }
            
           ij++;  /**************** Product of 2 matrices ******************/
         }  
         if (ij > ncodemax[j]) break;  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
       }    {
     }    /* 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 (k=0; k<19; k++) Ndum[k]=0;       before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
  for (i=1; i<=ncovmodel-2; i++) {    int i, j, k;
       ij=Tvar[i];    for(i=nrl; i<= nrh; i++)
       Ndum[ij]++;      for(k=ncolol; k<=ncoloh; k++){
     }        out[i][k]=0.;
         for(j=ncl; j<=nch; j++)
  ij=1;          out[i][k] +=in[i][j]*b[j][k];
  for (i=1; i<=10; i++) {      }
    if((Ndum[i]!=0) && (i<=ncovcol)){    return out;
      Tvaraff[ij]=i;  }
      ij++;  
    }  
  }  /************* Higher Matrix Product ***************/
    
     cptcoveff=ij-1;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
 }  {
     /* Computes the transition matrix starting at age 'age' over 
 /*********** Health Expectancies ****************/       'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )       nhstepm*hstepm matrices. 
        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 
   /* Health expectancies */       for the memory).
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;       Model is determined by parameters x and covariates have to be 
   double age, agelim, hf;       included manually here. 
   double ***p3mat,***varhe;  
   double **dnewm,**doldm;       */
   double *xp;  
   double **gp, **gm;    int i, j, d, h, k;
   double ***gradg, ***trgradg;    double **out, cov[NCOVMAX+1];
   int theta;    double **newm;
   
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    /* Hstepm could be zero and should return the unit matrix */
   xp=vector(1,npar);    for (i=1;i<=nlstate+ndeath;i++)
   dnewm=matrix(1,nlstate*2,1,npar);      for (j=1;j<=nlstate+ndeath;j++){
   doldm=matrix(1,nlstate*2,1,nlstate*2);        oldm[i][j]=(i==j ? 1.0 : 0.0);
          po[i][j][0]=(i==j ? 1.0 : 0.0);
   fprintf(ficreseij,"# Health expectancies\n");      }
   fprintf(ficreseij,"# Age");    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for(i=1; i<=nlstate;i++)    for(h=1; h <=nhstepm; h++){
     for(j=1; j<=nlstate;j++)      for(d=1; d <=hstepm; d++){
       fprintf(ficreseij," %1d-%1d (SE)",i,j);        newm=savm;
   fprintf(ficreseij,"\n");        /* Covariates have to be included here again */
         cov[1]=1.;
   if(estepm < stepm){        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     printf ("Problem %d lower than %d\n",estepm, stepm);        for (k=1; k<=cptcovn;k++) 
   }          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   else  hstepm=estepm;          for (k=1; k<=cptcovage;k++)
   /* We compute the life expectancy from trapezoids spaced every estepm months          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
    * This is mainly to measure the difference between two models: for example        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
    * if stepm=24 months pijx are given only every 2 years and by summing them          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
    * we are calculating an estimate of the Life Expectancy assuming a linear  
    * progression inbetween and thus overestimating or underestimating according  
    * to the curvature of the survival function. If, for the same date, we        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
    * estimate the model with stepm=1 month, we can keep estepm to 24 months        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
    * to compare the new estimate of Life expectancy with the same linear        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
    * hypothesis. A more precise result, taking into account a more precise                     pmij(pmmij,cov,ncovmodel,x,nlstate));
    * curvature will be obtained if estepm is as small as stepm. */        savm=oldm;
         oldm=newm;
   /* For example we decided to compute the life expectancy with the smallest unit */      }
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      for(i=1; i<=nlstate+ndeath; i++)
      nhstepm is the number of hstepm from age to agelim        for(j=1;j<=nlstate+ndeath;j++) {
      nstepm is the number of stepm from age to agelin.          po[i][j][h]=newm[i][j];
      Look at hpijx to understand the reason of that which relies in memory size          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
      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("h=%d ",h);*/
      survival function given by stepm (the optimization length). Unfortunately it    } /* end h */
      means that if the survival funtion is printed only each two years of age and if  /*     printf("\n H=%d \n",h); */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    return po;
      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 */  
   /*************** log-likelihood *************/
   agelim=AGESUP;  double func( double *x)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  {
     /* nhstepm age range expressed in number of stepm */    int i, ii, j, k, mi, d, kk;
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    double **out;
     /* if (stepm >= YEARM) hstepm=1;*/    double sw; /* Sum of weights */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    double lli; /* Individual log likelihood */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int s1, s2;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);    double bbh, survp;
     gp=matrix(0,nhstepm,1,nlstate*2);    long ipmx;
     gm=matrix(0,nhstepm,1,nlstate*2);    /*extern weight */
     /* We are differentiating ll according to initial status */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    /*for(i=1;i<imx;i++) 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        printf(" %d\n",s[4][i]);
      */
     cov[1]=1.;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
     /* Computing Variances of health expectancies */  
     if(mle==1){
      for(theta=1; theta <=npar; theta++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(i=1; i<=npar; i++){        /* Computes the values of the ncovmodel covariates of the model
         xp[i] = x[i] + (i==theta ?delti[theta]:0);           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
       }           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);             to be observed in j being in i according to the model.
           */
       cptj=0;        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
       for(j=1; j<= nlstate; j++){          cov[2+k]=covar[Tvar[k]][i];
         for(i=1; i<=nlstate; i++){        }
           cptj=cptj+1;        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){           is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;           has been calculated etc */
           }        for(mi=1; mi<= wav[i]-1; mi++){
         }          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
                    oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                    savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1; i<=npar; i++)            }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          for(d=0; d<dh[mi][i]; d++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              newm=savm;
                  cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       cptj=0;            for (kk=1; kk<=cptcovage;kk++) {
       for(j=1; j<= nlstate; j++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
         for(i=1;i<=nlstate;i++){            }
           cptj=cptj+1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;            savm=oldm;
           }            oldm=newm;
         }          } /* end mult */
       }        
       for(j=1; j<= nlstate*2; j++)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         for(h=0; h<=nhstepm-1; h++){          /* But now since version 0.9 we anticipate for bias at large stepm.
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         }           * (in months) between two waves is not a multiple of stepm, we rounded to 
      }           * the nearest (and in case of equal distance, to the lowest) interval but now
               * we keep into memory the bias bh[mi][i] and also the previous matrix product
 /* End theta */           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
      for(h=0; h<=nhstepm-1; h++)           * For stepm=1 the results are the same as for previous versions of Imach.
       for(j=1; j<=nlstate*2;j++)           * For stepm > 1 the results are less biased than in previous versions. 
         for(theta=1; theta <=npar; theta++)           */
           trgradg[h][j][theta]=gradg[h][theta][j];          s1=s[mw[mi][i]][i];
                s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
      for(i=1;i<=nlstate*2;i++)          /* bias bh is positive if real duration
       for(j=1;j<=nlstate*2;j++)           * is higher than the multiple of stepm and negative otherwise.
         varhe[i][j][(int)age] =0.;           */
           /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
      printf("%d|",(int)age);fflush(stdout);          if( s2 > nlstate){ 
      for(h=0;h<=nhstepm-1;h++){            /* i.e. if s2 is a death state and if the date of death is known 
       for(k=0;k<=nhstepm-1;k++){               then the contribution to the likelihood is the probability to 
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);               die between last step unit time and current  step unit time, 
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);               which is also equal to probability to die before dh 
         for(i=1;i<=nlstate*2;i++)               minus probability to die before dh-stepm . 
           for(j=1;j<=nlstate*2;j++)               In version up to 0.92 likelihood was computed
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;          as if date of death was unknown. Death was treated as any other
       }          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
                (healthy, disable or death) and IMaCh was corrected; but when we
     /* Computing expectancies */          introduced the exact date of death then we should have modified
     for(i=1; i<=nlstate;i++)          the contribution of an exact death to the likelihood. This new
       for(j=1; j<=nlstate;j++)          contribution is smaller and very dependent of the step unit
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          stepm. It is no more the probability to die between last interview
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;          and month of death but the probability to survive from last
                    interview up to one month before death multiplied by the
 /* 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]);*/          probability to die within a month. Thanks to Chris
           Jackson for correcting this bug.  Former versions increased
         }          mortality artificially. The bad side is that we add another loop
           which slows down the processing. The difference can be up to 10%
     fprintf(ficreseij,"%3.0f",age );          lower mortality.
     cptj=0;            */
     for(i=1; i<=nlstate;i++)            lli=log(out[s1][s2] - savm[s1][s2]);
       for(j=1; j<=nlstate;j++){  
         cptj++;  
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );          } else if  (s2==-2) {
       }            for (j=1,survp=0. ; j<=nlstate; j++) 
     fprintf(ficreseij,"\n");              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                /*survp += out[s1][j]; */
     free_matrix(gm,0,nhstepm,1,nlstate*2);            lli= log(survp);
     free_matrix(gp,0,nhstepm,1,nlstate*2);          }
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);          
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          else if  (s2==-4) { 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for (j=3,survp=0. ; j<=nlstate; j++)  
   }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
   free_vector(xp,1,npar);            lli= log(survp); 
   free_matrix(dnewm,1,nlstate*2,1,npar);          } 
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);  
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);          else if  (s2==-5) { 
 }            for (j=1,survp=0. ; j<=2; j++)  
               survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
 /************ Variance ******************/            lli= log(survp); 
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)          } 
 {          
   /* Variance of health expectancies */          else{
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double **newm;            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   double **dnewm,**doldm;          } 
   int i, j, nhstepm, hstepm, h, nstepm ;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   int k, cptcode;          /*if(lli ==000.0)*/
   double *xp;          /*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); */
   double **gp, **gm;          ipmx +=1;
   double ***gradg, ***trgradg;          sw += weight[i];
   double ***p3mat;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double age,agelim, hf;        } /* end of wave */
   int theta;      } /* end of individual */
     }  else if(mle==2){
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   fprintf(ficresvij,"# Age");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for(i=1; i<=nlstate;i++)        for(mi=1; mi<= wav[i]-1; mi++){
     for(j=1; j<=nlstate;j++)          for (ii=1;ii<=nlstate+ndeath;ii++)
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            for (j=1;j<=nlstate+ndeath;j++){
   fprintf(ficresvij,"\n");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
   xp=vector(1,npar);            }
   dnewm=matrix(1,nlstate,1,npar);          for(d=0; d<=dh[mi][i]; d++){
   doldm=matrix(1,nlstate,1,nlstate);            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   if(estepm < stepm){            for (kk=1; kk<=cptcovage;kk++) {
     printf ("Problem %d lower than %d\n",estepm, stepm);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
   else  hstepm=estepm;              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   /* For example we decided to compute the life expectancy with the smallest unit */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.            savm=oldm;
      nhstepm is the number of hstepm from age to agelim            oldm=newm;
      nstepm is the number of stepm from age to agelin.          } /* end mult */
      Look at hpijx to understand the reason of that which relies in memory size        
      and note for a fixed period like k years */          s1=s[mw[mi][i]][i];
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          s2=s[mw[mi+1][i]][i];
      survival function given by stepm (the optimization length). Unfortunately it          bbh=(double)bh[mi][i]/(double)stepm; 
      means that if the survival funtion is printed only each two years of age and if          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 */
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          ipmx +=1;
      results. So we changed our mind and took the option of the best precision.          sw += weight[i];
   */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        } /* end of wave */
   agelim = AGESUP;      } /* end of individual */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    }  else if(mle==3){  /* exponential inter-extrapolation */
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(mi=1; mi<= wav[i]-1; mi++){
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          for (ii=1;ii<=nlstate+ndeath;ii++)
     gp=matrix(0,nhstepm,1,nlstate);            for (j=1;j<=nlstate+ndeath;j++){
     gm=matrix(0,nhstepm,1,nlstate);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(theta=1; theta <=npar; theta++){            }
       for(i=1; i<=npar; i++){ /* Computes gradient */          for(d=0; d<dh[mi][i]; d++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            newm=savm;
       }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              for (kk=1; kk<=cptcovage;kk++) {
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
       if (popbased==1) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for(i=1; i<=nlstate;i++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           prlim[i][i]=probs[(int)age][i][ij];            savm=oldm;
       }            oldm=newm;
            } /* end mult */
       for(j=1; j<= nlstate; j++){        
         for(h=0; h<=nhstepm; h++){          s1=s[mw[mi][i]][i];
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          bbh=(double)bh[mi][i]/(double)stepm; 
         }          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       }          ipmx +=1;
              sw += weight[i];
       for(i=1; i<=npar; i++) /* Computes gradient */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        } /* end of wave */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        } /* end of individual */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       if (popbased==1) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(i=1; i<=nlstate;i++)        for(mi=1; mi<= wav[i]-1; mi++){
           prlim[i][i]=probs[(int)age][i][ij];          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<= nlstate; j++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(h=0; h<=nhstepm; h++){            }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          for(d=0; d<dh[mi][i]; d++){
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(j=1; j<= nlstate; j++)            }
         for(h=0; h<=nhstepm; h++){          
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     } /* End theta */            savm=oldm;
             oldm=newm;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          } /* end mult */
         
     for(h=0; h<=nhstepm; h++)          s1=s[mw[mi][i]][i];
       for(j=1; j<=nlstate;j++)          s2=s[mw[mi+1][i]][i];
         for(theta=1; theta <=npar; theta++)          if( s2 > nlstate){ 
           trgradg[h][j][theta]=gradg[h][theta][j];            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     for(i=1;i<=nlstate;i++)          }
       for(j=1;j<=nlstate;j++)          ipmx +=1;
         vareij[i][j][(int)age] =0.;          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(h=0;h<=nhstepm;h++){  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       for(k=0;k<=nhstepm;k++){        } /* end of wave */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      } /* end of individual */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
         for(i=1;i<=nlstate;i++)      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];
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
     }            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     fprintf(ficresvij,"%.0f ",age );              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i=1; i<=nlstate;i++)            }
       for(j=1; j<=nlstate;j++){          for(d=0; d<dh[mi][i]; d++){
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);            newm=savm;
       }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     fprintf(ficresvij,"\n");            for (kk=1; kk<=cptcovage;kk++) {
     free_matrix(gp,0,nhstepm,1,nlstate);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     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);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   } /* End age */            savm=oldm;
              oldm=newm;
   free_vector(xp,1,npar);          } /* end mult */
   free_matrix(doldm,1,nlstate,1,npar);        
   free_matrix(dnewm,1,nlstate,1,nlstate);          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
 /************ Variance of prevlim ******************/          sw += weight[i];
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)          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]);*/
   /* Variance of prevalence limit */        } /* end of wave */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      } /* end of individual */
   double **newm;    } /* End of if */
   double **dnewm,**doldm;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   int i, j, nhstepm, hstepm;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   int k, cptcode;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   double *xp;    return -l;
   double *gp, *gm;  }
   double **gradg, **trgradg;  
   double age,agelim;  /*************** log-likelihood *************/
   int theta;  double funcone( double *x)
      {
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");    /* Same as likeli but slower because of a lot of printf and if */
   fprintf(ficresvpl,"# Age");    int i, ii, j, k, mi, d, kk;
   for(i=1; i<=nlstate;i++)    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
       fprintf(ficresvpl," %1d-%1d",i,i);    double **out;
   fprintf(ficresvpl,"\n");    double lli; /* Individual log likelihood */
     double llt;
   xp=vector(1,npar);    int s1, s2;
   dnewm=matrix(1,nlstate,1,npar);    double bbh, survp;
   doldm=matrix(1,nlstate,1,nlstate);    /*extern weight */
      /* We are differentiating ll according to initial status */
   hstepm=1*YEARM; /* Every year of age */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    /*for(i=1;i<imx;i++) 
   agelim = AGESUP;      printf(" %d\n",s[4][i]);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    cov[1]=1.;
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    for(k=1; k<=nlstate; k++) ll[k]=0.;
     gradg=matrix(1,npar,1,nlstate);  
     gp=vector(1,nlstate);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     gm=vector(1,nlstate);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
     for(theta=1; theta <=npar; theta++){        for (ii=1;ii<=nlstate+ndeath;ii++)
       for(i=1; i<=npar; i++){ /* Computes gradient */          for (j=1;j<=nlstate+ndeath;j++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          }
       for(i=1;i<=nlstate;i++)        for(d=0; d<dh[mi][i]; d++){
         gp[i] = prlim[i][i];          newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(i=1; i<=npar; i++) /* Computes gradient */          for (kk=1; kk<=cptcovage;kk++) {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          }
       for(i=1;i<=nlstate;i++)          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         gm[i] = prlim[i][i];          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(i=1;i<=nlstate;i++)          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
     } /* End theta */          savm=oldm;
           oldm=newm;
     trgradg =matrix(1,nlstate,1,npar);        } /* end mult */
         
     for(j=1; j<=nlstate;j++)        s1=s[mw[mi][i]][i];
       for(theta=1; theta <=npar; theta++)        s2=s[mw[mi+1][i]][i];
         trgradg[j][theta]=gradg[theta][j];        bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
     for(i=1;i<=nlstate;i++)         * is higher than the multiple of stepm and negative otherwise.
       varpl[i][(int)age] =0.;         */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          lli=log(out[s1][s2] - savm[s1][s2]);
     for(i=1;i<=nlstate;i++)        } else if  (s2==-2) {
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          for (j=1,survp=0. ; j<=nlstate; j++) 
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     fprintf(ficresvpl,"%.0f ",age );          lli= log(survp);
     for(i=1; i<=nlstate;i++)        }else if (mle==1){
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     fprintf(ficresvpl,"\n");        } else if(mle==2){
     free_vector(gp,1,nlstate);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     free_vector(gm,1,nlstate);        } else if(mle==3){  /* exponential inter-extrapolation */
     free_matrix(gradg,1,npar,1,nlstate);          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 */
     free_matrix(trgradg,1,nlstate,1,npar);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   } /* End age */          lli=log(out[s1][s2]); /* Original formula */
         } else{  /* mle=0 back to 1 */
   free_vector(xp,1,npar);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   free_matrix(doldm,1,nlstate,1,npar);          /*lli=log(out[s1][s2]); */ /* Original formula */
   free_matrix(dnewm,1,nlstate,1,nlstate);        } /* End of if */
         ipmx +=1;
 }        sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /************ Variance of one-step probabilities  ******************/        /*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]); */
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)        if(globpr){
 {          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   int i, j, i1, k1, j1, z1;   %11.6f %11.6f %11.6f ", \
   int k=0,l, cptcode;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   double **dnewm,**doldm;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   double *xp;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   double *gp, *gm;            llt +=ll[k]*gipmx/gsw;
   double **gradg, **trgradg;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   double age,agelim, cov[NCOVMAX];          }
   int theta;          fprintf(ficresilk," %10.6f\n", -llt);
   char fileresprob[FILENAMELENGTH];        }
   char fileresprobcov[FILENAMELENGTH];      } /* end of wave */
   char fileresprobcor[FILENAMELENGTH];    } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   strcpy(fileresprob,"prob");    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   strcat(fileresprob,fileres);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    if(globpr==0){ /* First time we count the contributions and weights */
     printf("Problem with resultfile: %s\n", fileresprob);      gipmx=ipmx;
   }      gsw=sw;
   strcpy(fileresprobcov,"probcov");    }
   strcat(fileresprobcov,fileres);    return -l;
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {  }
     printf("Problem with resultfile: %s\n", fileresprobcov);  
   }  
   strcpy(fileresprobcor,"probcor");  /*************** function likelione ***********/
   strcat(fileresprobcor,fileres);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {  {
     printf("Problem with resultfile: %s\n", fileresprobcor);    /* This routine should help understanding what is done with 
   }       the selection of individuals/waves and
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);       to check the exact contribution to the likelihood.
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);       Plotting could be done.
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);     */
      int k;
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");  
   fprintf(ficresprob,"# Age");    if(*globpri !=0){ /* Just counts and sums, no printings */
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");      strcpy(fileresilk,"ilk"); 
   fprintf(ficresprobcov,"# Age");      strcat(fileresilk,fileres);
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   fprintf(ficresprobcov,"# Age");        printf("Problem with resultfile: %s\n", fileresilk);
   for(i=1; i<=nlstate;i++)        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     for(j=1; j<=(nlstate+ndeath);j++){      }
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
       fprintf(ficresprobcov," p%1d-%1d ",i,j);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       fprintf(ficresprobcor," p%1d-%1d ",i,j);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     }        for(k=1; k<=nlstate; k++) 
   fprintf(ficresprob,"\n");        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   fprintf(ficresprobcov,"\n");      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   fprintf(ficresprobcor,"\n");    }
   xp=vector(1,npar);  
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    *fretone=(*funcone)(p);
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    if(*globpri !=0){
        fclose(ficresilk);
   cov[1]=1;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   j=cptcoveff;      fflush(fichtm); 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    } 
   j1=0;    return;
   for(k1=1; k1<=1;k1++){  }
     for(i1=1; i1<=ncodemax[k1];i1++){  
     j1++;  
   /*********** Maximum Likelihood Estimation ***************/
     if  (cptcovn>0) {  
       fprintf(ficresprob, "\n#********** Variable ");  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       fprintf(ficresprobcov, "\n#********** Variable ");  {
       fprintf(ficresprobcor, "\n#********** Variable ");    int i,j, iter;
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double **xi;
       fprintf(ficresprob, "**********\n#");    double fret;
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    double fretone; /* Only one call to likelihood */
       fprintf(ficresprobcov, "**********\n#");    /*  char filerespow[FILENAMELENGTH];*/
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    xi=matrix(1,npar,1,npar);
       fprintf(ficresprobcor, "**********\n#");    for (i=1;i<=npar;i++)
     }      for (j=1;j<=npar;j++)
            xi[i][j]=(i==j ? 1.0 : 0.0);
       for (age=bage; age<=fage; age ++){    printf("Powell\n");  fprintf(ficlog,"Powell\n");
         cov[2]=age;    strcpy(filerespow,"pow"); 
         for (k=1; k<=cptcovn;k++) {    strcat(filerespow,fileres);
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    if((ficrespow=fopen(filerespow,"w"))==NULL) {
         }      printf("Problem with resultfile: %s\n", filerespow);
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         for (k=1; k<=cptcovprod;k++)    }
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    fprintf(ficrespow,"# Powell\n# iter -2*LL");
            for (i=1;i<=nlstate;i++)
         gradg=matrix(1,npar,1,9);      for(j=1;j<=nlstate+ndeath;j++)
         trgradg=matrix(1,9,1,npar);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    fprintf(ficrespow,"\n");
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));  
        powell(p,xi,npar,ftol,&iter,&fret,func);
         for(theta=1; theta <=npar; theta++){  
           for(i=1; i<=npar; i++)    free_matrix(xi,1,npar,1,npar);
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    fclose(ficrespow);
              printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
              fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           k=0;  
           for(i=1; i<= (nlstate+ndeath); i++){  }
             for(j=1; j<=(nlstate+ndeath);j++){  
               k=k+1;  /**** Computes Hessian and covariance matrix ***/
               gp[k]=pmmij[i][j];  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
             }  {
           }    double  **a,**y,*x,pd;
              double **hess;
           for(i=1; i<=npar; i++)    int i, j,jk;
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    int *indx;
      
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
           k=0;    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
           for(i=1; i<=(nlstate+ndeath); i++){    void lubksb(double **a, int npar, int *indx, double b[]) ;
             for(j=1; j<=(nlstate+ndeath);j++){    void ludcmp(double **a, int npar, int *indx, double *d) ;
               k=k+1;    double gompertz(double p[]);
               gm[k]=pmmij[i][j];    hess=matrix(1,npar,1,npar);
             }  
           }    printf("\nCalculation of the hessian matrix. Wait...\n");
          fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    for (i=1;i<=npar;i++){
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        printf("%d",i);fflush(stdout);
         }      fprintf(ficlog,"%d",i);fflush(ficlog);
      
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
           for(theta=1; theta <=npar; theta++)      
             trgradg[j][theta]=gradg[theta][j];      /*  printf(" %f ",p[i]);
                  printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    }
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    
            for (i=1;i<=npar;i++) {
         pmij(pmmij,cov,ncovmodel,x,nlstate);      for (j=1;j<=npar;j++)  {
                if (j>i) { 
         k=0;          printf(".%d%d",i,j);fflush(stdout);
         for(i=1; i<=(nlstate+ndeath); i++){          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           for(j=1; j<=(nlstate+ndeath);j++){          hess[i][j]=hessij(p,delti,i,j,func,npar);
             k=k+1;          
             gm[k]=pmmij[i][j];          hess[j][i]=hess[i][j];    
           }          /*printf(" %lf ",hess[i][j]);*/
         }        }
            }
         /*printf("\n%d ",(int)age);    }
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    printf("\n");
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    fprintf(ficlog,"\n");
      }*/  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         fprintf(ficresprob,"\n%d ",(int)age);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
         fprintf(ficresprobcov,"\n%d ",(int)age);    
         fprintf(ficresprobcor,"\n%d ",(int)age);    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)    x=vector(1,npar);
           fprintf(ficresprob,"%12.3e (%12.3e) ",gm[i],sqrt(doldm[i][j]));    indx=ivector(1,npar);
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    for (i=1;i<=npar;i++)
           fprintf(ficresprobcov,"%12.3e ",gm[i]);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
           fprintf(ficresprobcor,"%12.3e ",gm[i]);    ludcmp(a,npar,indx,&pd);
         }  
         i=0;    for (j=1;j<=npar;j++) {
         for (k=1; k<=(nlstate);k++){      for (i=1;i<=npar;i++) x[i]=0;
           for (l=1; l<=(nlstate+ndeath);l++){      x[j]=1;
             i=i++;      lubksb(a,npar,indx,x);
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);      for (i=1;i<=npar;i++){ 
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);        matcov[i][j]=x[i];
             for (j=1; j<=i;j++){      }
               fprintf(ficresprobcov," %12.3e",doldm[i][j]);    }
               fprintf(ficresprobcor," %12.3e",doldm[i][j]/sqrt(doldm[i][i])/sqrt(doldm[j][j]));  
             }    printf("\n#Hessian matrix#\n");
           }    fprintf(ficlog,"\n#Hessian matrix#\n");
         }    for (i=1;i<=npar;i++) { 
       }      for (j=1;j<=npar;j++) { 
     }        printf("%.3e ",hess[i][j]);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        fprintf(ficlog,"%.3e ",hess[i][j]);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      }
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      printf("\n");
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      fprintf(ficlog,"\n");
   }    }
   free_vector(xp,1,npar);  
   fclose(ficresprob);    /* Recompute Inverse */
   fclose(ficresprobcov);    for (i=1;i<=npar;i++)
   fclose(ficresprobcor);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
 }    ludcmp(a,npar,indx,&pd);
   
     /*  printf("\n#Hessian matrix recomputed#\n");
 /******************* Printing html file ***********/  
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    for (j=1;j<=npar;j++) {
                   int lastpass, int stepm, int weightopt, char model[],\      for (i=1;i<=npar;i++) x[i]=0;
                   int imx,int jmin, int jmax, double jmeanint,char optionfile[], \      x[j]=1;
                   char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\      lubksb(a,npar,indx,x);
                   char version[], int popforecast, int estepm ,\      for (i=1;i<=npar;i++){ 
                   double jprev1, double mprev1,double anprev1, \        y[i][j]=x[i];
                   double jprev2, double mprev2,double anprev2){        printf("%.3e ",y[i][j]);
   int jj1, k1, i1, cpt;        fprintf(ficlog,"%.3e ",y[i][j]);
   FILE *fichtm;      }
   /*char optionfilehtm[FILENAMELENGTH];*/      printf("\n");
       fprintf(ficlog,"\n");
   strcpy(optionfilehtm,optionfile);    }
   strcat(optionfilehtm,".htm");    */
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm), exit(0);    free_matrix(a,1,npar,1,npar);
   }    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    free_ivector(indx,1,npar);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    free_matrix(hess,1,npar,1,npar);
 \n  
 Total number of observations=%d <br>\n  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n  }
 <hr  size=\"2\" color=\"#EC5E5E\">  
  <ul><li>Parameter files<br>\n  /*************** hessian matrix ****************/
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);  {
     int i;
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n    int l=1, lmax=20;
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n    double k1,k2;
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    double p2[MAXPARM+1]; /* identical to x */
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n    double res;
  - Life expectancies by age and initial health status (estepm=%2d months):    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
    <a href=\"e%s\">e%s</a> <br>\n</li>", \    double fx;
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    int k=0,kmax=10;
     double l1;
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n  
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n    fx=func(x);
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    for (i=1;i<=npar;i++) p2[i]=x[i];
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n      l1=pow(10,l);
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n      delts=delt;
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n      for(k=1 ; k <kmax; k=k+1){
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);        delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
  if(popforecast==1) fprintf(fichtm,"\n        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n        p2[theta]=x[theta]-delt;
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n        k2=func(p2)-fx;
         <br>",fileres,fileres,fileres,fileres);        /*res= (k1-2.0*fx+k2)/delt/delt; */
  else        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
    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);        
 fprintf(fichtm," <li>Graphs</li><p>");  #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);
  m=cptcoveff;        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);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  #endif
         /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
  jj1=0;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
  for(k1=1; k1<=m;k1++){          k=kmax;
    for(i1=1; i1<=ncodemax[k1];i1++){        }
      jj1++;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
      if (cptcovn > 0) {          k=kmax; l=lmax*10.;
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        }
        for (cpt=1; cpt<=cptcoveff;cpt++)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);          delts=delt;
        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: pe%s%d1.png<br>    delti[theta]=delts;
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        return res; 
      /* 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: pe%s%d2.png<br>  }
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  
        /* Stable prevalence in each health state */  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
        for(cpt=1; cpt<nlstate;cpt++){  {
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    int i;
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    int l=1, l1, lmax=20;
        }    double k1,k2,k3,k4,res,fx;
     for(cpt=1; cpt<=nlstate;cpt++) {    double p2[MAXPARM+1];
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    int k;
 interval) in state (%d): v%s%d%d.png <br>  
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      fx=func(x);
      }    for (k=1; k<=2; k++) {
      for(cpt=1; cpt<=nlstate;cpt++) {      for (i=1;i<=npar;i++) p2[i]=x[i];
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>      p2[thetai]=x[thetai]+delti[thetai]/k;
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
      }      k1=func(p2)-fx;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    
 health expectancies in states (1) and (2): e%s%d.png<br>      p2[thetai]=x[thetai]+delti[thetai]/k;
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 fprintf(fichtm,"\n</body>");      k2=func(p2)-fx;
    }    
  }      p2[thetai]=x[thetai]-delti[thetai]/k;
 fclose(fichtm);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 }      k3=func(p2)-fx;
     
 /******************* Gnuplot file **************/      p2[thetai]=x[thetai]-delti[thetai]/k;
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k4=func(p2)-fx;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   int ng;  #ifdef DEBUG
   strcpy(optionfilegnuplot,optionfilefiname);      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);
   strcat(optionfilegnuplot,".gp");      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);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  #endif
     printf("Problem with file %s",optionfilegnuplot);    }
   }    return res;
   }
 #ifdef windows  
     fprintf(ficgp,"cd \"%s\" \n",pathc);  /************** Inverse of matrix **************/
 #endif  void ludcmp(double **a, int n, int *indx, double *d) 
 m=pow(2,cptcoveff);  { 
      int i,imax,j,k; 
  /* 1eme*/    double big,dum,sum,temp; 
   for (cpt=1; cpt<= nlstate ; cpt ++) {    double *vv; 
    for (k1=1; k1<= m ; k1 ++) {   
     vv=vector(1,n); 
 #ifdef windows    *d=1.0; 
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    for (i=1;i<=n;i++) { 
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);      big=0.0; 
 #endif      for (j=1;j<=n;j++) 
 #ifdef unix        if ((temp=fabs(a[i][j])) > big) big=temp; 
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);      vv[i]=1.0/big; 
 #endif    } 
     for (j=1;j<=n;j++) { 
 for (i=1; i<= nlstate ; i ++) {      for (i=1;i<j;i++) { 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        sum=a[i][j]; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
 }        a[i][j]=sum; 
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      } 
     for (i=1; i<= nlstate ; i ++) {      big=0.0; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for (i=j;i<=n;i++) { 
   else fprintf(ficgp," \%%*lf (\%%*lf)");        sum=a[i][j]; 
 }        for (k=1;k<j;k++) 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          sum -= a[i][k]*a[k][j]; 
      for (i=1; i<= nlstate ; i ++) {        a[i][j]=sum; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          big=dum; 
 }            imax=i; 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        } 
 #ifdef unix      } 
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");      if (j != imax) { 
 #endif        for (k=1;k<=n;k++) { 
    }          dum=a[imax][k]; 
   }          a[imax][k]=a[j][k]; 
   /*2 eme*/          a[j][k]=dum; 
         } 
   for (k1=1; k1<= m ; k1 ++) {        *d = -(*d); 
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);        vv[imax]=vv[j]; 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);      } 
          indx[j]=imax; 
     for (i=1; i<= nlstate+1 ; i ++) {      if (a[j][j] == 0.0) a[j][j]=TINY; 
       k=2*i;      if (j != n) { 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        dum=1.0/(a[j][j]); 
       for (j=1; j<= nlstate+1 ; j ++) {        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    } 
 }      free_vector(vv,1,n);  /* Doesn't work */
       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 (j=1; j<= nlstate+1 ; j ++) {  void lubksb(double **a, int n, int *indx, double b[]) 
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  { 
         else fprintf(ficgp," \%%*lf (\%%*lf)");    int i,ii=0,ip,j; 
 }      double sum; 
       fprintf(ficgp,"\" t\"\" w l 0,");   
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    for (i=1;i<=n;i++) { 
       for (j=1; j<= nlstate+1 ; j ++) {      ip=indx[i]; 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      sum=b[ip]; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      b[ip]=b[i]; 
 }        if (ii) 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else fprintf(ficgp,"\" t\"\" w l 0,");      else if (sum) ii=i; 
     }      b[i]=sum; 
   }    } 
      for (i=n;i>=1;i--) { 
   /*3eme*/      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   for (k1=1; k1<= m ; k1 ++) {      b[i]=sum/a[i][i]; 
     for (cpt=1; cpt<= nlstate ; cpt ++) {    } 
       k=2+nlstate*(2*cpt-2);  } 
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);  void pstamp(FILE *fichier)
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  {
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  }
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");  /************ Frequencies ********************/
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
   {  /* Some frequencies */
 */    
       for (i=1; i< nlstate ; i ++) {    int i, m, jk, k1,i1, j1, bool, z1,j;
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);    int first;
     double ***freq; /* Frequencies */
       }    double *pp, **prop;
     }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   }    char fileresp[FILENAMELENGTH];
      
   /* CV preval stat */    pp=vector(1,nlstate);
     for (k1=1; k1<= m ; k1 ++) {    prop=matrix(1,nlstate,iagemin,iagemax+3);
     for (cpt=1; cpt<nlstate ; cpt ++) {    strcpy(fileresp,"p");
       k=3;    strcat(fileresp,fileres);
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    if((ficresp=fopen(fileresp,"w"))==NULL) {
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       for (i=1; i< nlstate ; i ++)      exit(0);
         fprintf(ficgp,"+$%d",k+i+1);    }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
          j1=0;
       l=3+(nlstate+ndeath)*cpt;    
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    j=cptcoveff;
       for (i=1; i< nlstate ; i ++) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);    first=1;
       }  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
     }    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
   }      /*    j1++;
    */
   /* proba elementaires */    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
    for(i=1,jk=1; i <=nlstate; i++){        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     for(k=1; k <=(nlstate+ndeath); k++){          scanf("%d", i);*/
       if (k != i) {        for (i=-5; i<=nlstate+ndeath; i++)  
         for(j=1; j <=ncovmodel; j++){          for (jk=-5; jk<=nlstate+ndeath; jk++)  
                    for(m=iagemin; m <= iagemax+3; m++)
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);              freq[i][jk][m]=0;
           jk++;        
           fprintf(ficgp,"\n");        for (i=1; i<=nlstate; i++)  
         }          for(m=iagemin; m <= iagemax+3; m++)
       }            prop[i][m]=0;
     }        
    }        dateintsum=0;
         k2cpt=0;
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/        for (i=1; i<=imx; i++) {
      for(jk=1; jk <=m; jk++) {          bool=1;
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
        if (ng==2)            for (z1=1; z1<=cptcoveff; z1++)       
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
        else                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
          fprintf(ficgp,"\nset title \"Probability\"\n");                bool=0;
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);                /* 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", 
        i=1;                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
        for(k2=1; k2<=nlstate; k2++) {                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
          k3=i;                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
          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);          if (bool==1){
              else            for(m=firstpass; m<=lastpass; m++){
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);              k2=anint[m][i]+(mint[m][i]/12.);
              ij=1;              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
              for(j=3; j <=ncovmodel; j++) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                  ij++;                if (m<lastpass) {
                }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                else                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                }
              }                
              fprintf(ficgp,")/(1");                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                                dateintsum=dateintsum+k2;
              for(k1=1; k1 <=nlstate; k1++){                    k2cpt++;
                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]]]);        } /* end i */
                    ij++;         
                  }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
                  else        pstamp(ficresp);
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        if  (cptcovn>0) {
                }          fprintf(ficresp, "\n#********** Variable "); 
                fprintf(ficgp,")");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
              }          fprintf(ficresp, "**********\n#");
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);          fprintf(ficlog, "\n#********** Variable "); 
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
              i=i+ncovmodel;          fprintf(ficlog, "**********\n#");
            }        }
          }        for(i=1; i<=nlstate;i++) 
        }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
      }        fprintf(ficresp, "\n");
    }        
    fclose(ficgp);        for(i=iagemin; i <= iagemax+3; i++){
 }  /* end gnuplot */          if(i==iagemax+3){
             fprintf(ficlog,"Total");
           }else{
 /*************** Moving average **************/            if(first==1){
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){              first=0;
               printf("See log file for details...\n");
   int i, cpt, cptcod;            }
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)            fprintf(ficlog,"Age %d", i);
       for (i=1; i<=nlstate;i++)          }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          for(jk=1; jk <=nlstate ; jk++){
           mobaverage[(int)agedeb][i][cptcod]=0.;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                  pp[jk] += freq[jk][m][i]; 
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          }
       for (i=1; i<=nlstate;i++){          for(jk=1; jk <=nlstate ; jk++){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            for(m=-1, pos=0; m <=0 ; m++)
           for (cpt=0;cpt<=4;cpt++){              pos += freq[jk][m][i];
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];            if(pp[jk]>=1.e-10){
           }              if(first==1){
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         }              }
       }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     }            }else{
                  if(first==1)
 }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
 /************** Forecasting ******************/          }
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){  
            for(jk=1; jk <=nlstate ; jk++){
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   int *popage;              pp[jk] += freq[jk][m][i];
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          }       
   double *popeffectif,*popcount;          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   double ***p3mat;            pos += pp[jk];
   char fileresf[FILENAMELENGTH];            posprop += prop[jk][i];
           }
  agelim=AGESUP;          for(jk=1; jk <=nlstate ; jk++){
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;            if(pos>=1.e-5){
               if(first==1)
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                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{
   strcpy(fileresf,"f");              if(first==1)
   strcat(fileresf,fileres);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   if((ficresf=fopen(fileresf,"w"))==NULL) {              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     printf("Problem with forecast resultfile: %s\n", fileresf);            }
   }            if( i <= iagemax){
   printf("Computing forecasting: result on file '%s' \n", fileresf);              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;                /*probs[i][jk][j1]= pp[jk]/pos;*/
                 /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   if (mobilav==1) {              }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              else
     movingaverage(agedeb, fage, ageminpar, mobaverage);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   }            }
           }
   stepsize=(int) (stepm+YEARM-1)/YEARM;          
   if (stepm<=12) stepsize=1;          for(jk=-1; jk <=nlstate+ndeath; jk++)
              for(m=-1; m <=nlstate+ndeath; m++)
   agelim=AGESUP;              if(freq[jk][m][i] !=0 ) {
                if(first==1)
   hstepm=1;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   hstepm=hstepm/stepm;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   yp1=modf(dateintmean,&yp);              }
   anprojmean=yp;          if(i <= iagemax)
   yp2=modf((yp1*12),&yp);            fprintf(ficresp,"\n");
   mprojmean=yp;          if(first==1)
   yp1=modf((yp2*30.5),&yp);            printf("Others in log...\n");
   jprojmean=yp;          fprintf(ficlog,"\n");
   if(jprojmean==0) jprojmean=1;        }
   if(mprojmean==0) jprojmean=1;        /*}*/
      }
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    dateintmean=dateintsum/k2cpt; 
     
   for(cptcov=1;cptcov<=i2;cptcov++){    fclose(ficresp);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
       k=k+1;    free_vector(pp,1,nlstate);
       fprintf(ficresf,"\n#******");    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       for(j=1;j<=cptcoveff;j++) {    /* End of Freq */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  }
       }  
       fprintf(ficresf,"******\n");  /************ Prevalence ********************/
       fprintf(ficresf,"# StartingAge FinalAge");  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  {  
          /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
             in each health status at the date of interview (if between dateprev1 and dateprev2).
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {       We still use firstpass and lastpass as another selection.
         fprintf(ficresf,"\n");    */
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);     
     int i, m, jk, k1, i1, j1, bool, z1,j;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    double ***freq; /* Frequencies */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    double *pp, **prop;
           nhstepm = nhstepm/hstepm;    double pos,posprop; 
              double  y2; /* in fractional years */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int iagemin, iagemax;
           oldm=oldms;savm=savms;    int first; /** to stop verbosity which is redirected to log file */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
            iagemin= (int) agemin;
           for (h=0; h<=nhstepm; h++){    iagemax= (int) agemax;
             if (h==(int) (calagedate+YEARM*cpt)) {    /*pp=vector(1,nlstate);*/
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
             }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
             for(j=1; j<=nlstate+ndeath;j++) {    j1=0;
               kk1=0.;kk2=0;    
               for(i=1; i<=nlstate;i++) {                  /*j=cptcoveff;*/
                 if (mobilav==1)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    
                 else {    first=1;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
                 }      /*for(i1=1; i1<=ncodemax[k1];i1++){
                        j1++;*/
               }        
               if (h==(int)(calagedate+12*cpt)){        for (i=1; i<=nlstate; i++)  
                 fprintf(ficresf," %.3f", kk1);          for(m=iagemin; m <= iagemax+3; m++)
                                    prop[i][m]=0.0;
               }       
             }        for (i=1; i<=imx; i++) { /* Each individual */
           }          bool=1;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if  (cptcovn>0) {
         }            for (z1=1; z1<=cptcoveff; z1++) 
       }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     }                bool=0;
   }          } 
                  if (bool==1) { 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
               y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   fclose(ficresf);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
 }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 /************** Forecasting ******************/                if(agev[m][i]==1) agev[m][i]=iagemax+2;
 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){                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) { 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                  /*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]]);*/
   int *popage;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;                  prop[s[m][i]][iagemax+3] += weight[i]; 
   double *popeffectif,*popcount;                } 
   double ***p3mat,***tabpop,***tabpopprev;              }
   char filerespop[FILENAMELENGTH];            } /* end selection of waves */
           }
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(i=iagemin; i <= iagemax+3; i++){  
   agelim=AGESUP;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;            posprop += prop[jk][i]; 
            } 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          
            for(jk=1; jk <=nlstate ; jk++){     
              if( i <=  iagemax){ 
   strcpy(filerespop,"pop");              if(posprop>=1.e-5){ 
   strcat(filerespop,fileres);                probs[i][jk][j1]= prop[jk][i]/posprop;
   if((ficrespop=fopen(filerespop,"w"))==NULL) {              } else{
     printf("Problem with forecast resultfile: %s\n", filerespop);                if(first==1){
   }                  first=0;
   printf("Computing forecasting: result on file '%s' \n", filerespop);                  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]);
                 }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;              }
             } 
   if (mobilav==1) {          }/* end jk */ 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }/* end i */ 
     movingaverage(agedeb, fage, ageminpar, mobaverage);      /*} *//* end i1 */
   }    } /* end j1 */
     
   stepsize=(int) (stepm+YEARM-1)/YEARM;    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   if (stepm<=12) stepsize=1;    /*free_vector(pp,1,nlstate);*/
      free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   agelim=AGESUP;  }  /* End of prevalence */
    
   hstepm=1;  /************* Waves Concatenation ***************/
   hstepm=hstepm/stepm;  
    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)
   if (popforecast==1) {  {
     if((ficpop=fopen(popfile,"r"))==NULL) {    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       printf("Problem with population file : %s\n",popfile);exit(0);       Death is a valid wave (if date is known).
     }       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     popage=ivector(0,AGESUP);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     popeffectif=vector(0,AGESUP);       and mw[mi+1][i]. dh depends on stepm.
     popcount=vector(0,AGESUP);       */
      
     i=1;      int i, mi, m;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
           double sum=0., jmean=0.;*/
     imx=i;    int first;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    int j, k=0,jk, ju, jl;
   }    double sum=0.;
     first=0;
   for(cptcov=1;cptcov<=i2;cptcov++){    jmin=1e+5;
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    jmax=-1;
       k=k+1;    jmean=0.;
       fprintf(ficrespop,"\n#******");    for(i=1; i<=imx; i++){
       for(j=1;j<=cptcoveff;j++) {      mi=0;
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      m=firstpass;
       }      while(s[m][i] <= nlstate){
       fprintf(ficrespop,"******\n");        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       fprintf(ficrespop,"# Age");          mw[++mi][i]=m;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);        if(m >=lastpass)
       if (popforecast==1)  fprintf(ficrespop," [Population]");          break;
              else
       for (cpt=0; cpt<=0;cpt++) {          m++;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        }/* end while */
              if (s[m][i] > nlstate){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        mi++;     /* Death is another wave */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        /* if(mi==0)  never been interviewed correctly before death */
           nhstepm = nhstepm/hstepm;           /* Only death is a correct wave */
                  mw[mi][i]=m;
           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);        wav[i]=mi;
              if(mi==0){
           for (h=0; h<=nhstepm; h++){        nbwarn++;
             if (h==(int) (calagedate+YEARM*cpt)) {        if(first==0){
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
             }          first=1;
             for(j=1; j<=nlstate+ndeath;j++) {        }
               kk1=0.;kk2=0;        if(first==1){
               for(i=1; i<=nlstate;i++) {                        fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
                 if (mobilav==1)        }
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      } /* end mi==0 */
                 else {    } /* End individuals */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  
                 }    for(i=1; i<=imx; i++){
               }      for(mi=1; mi<wav[i];mi++){
               if (h==(int)(calagedate+12*cpt)){        if (stepm <=0)
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;          dh[mi][i]=1;
                   /*fprintf(ficrespop," %.3f", kk1);        else{
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
               }            if (agedc[i] < 2*AGESUP) {
             }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
             for(i=1; i<=nlstate;i++){              if(j==0) j=1;  /* Survives at least one month after exam */
               kk1=0.;              else if(j<0){
                 for(j=1; j<=nlstate;j++){                nberr++;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 }                j=1; /* Temporary Dangerous patch */
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
             }                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)              }
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);              k=k+1;
           }              if (j >= jmax){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                jmax=j;
         }                ijmax=i;
       }              }
                if (j <= jmin){
   /******/                jmin=j;
                 ijmin=i;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {              }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                sum=sum+j;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           nhstepm = nhstepm/hstepm;            }
                    }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          else{
           oldm=oldms;savm=savms;            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    /*        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]); */
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {            k=k+1;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);            if (j >= jmax) {
             }              jmax=j;
             for(j=1; j<=nlstate+ndeath;j++) {              ijmax=i;
               kk1=0.;kk2=0;            }
               for(i=1; i<=nlstate;i++) {                          else if (j <= jmin){
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                  jmin=j;
               }              ijmin=i;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);            }
             }            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           }            /*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]);*/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            if(j<0){
         }              nberr++;
       }              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]);
    }              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   }            }
              sum=sum+j;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
           jk= j/stepm;
   if (popforecast==1) {          jl= j -jk*stepm;
     free_ivector(popage,0,AGESUP);          ju= j -(jk+1)*stepm;
     free_vector(popeffectif,0,AGESUP);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     free_vector(popcount,0,AGESUP);            if(jl==0){
   }              dh[mi][i]=jk;
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              bh[mi][i]=0;
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            }else{ /* We want a negative bias in order to only have interpolation ie
   fclose(ficrespop);                    * to avoid the price of an extra matrix product in likelihood */
 }              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
 /***********************************************/            }
 /**************** Main Program *****************/          }else{
 /***********************************************/            if(jl <= -ju){
               dh[mi][i]=jk;
 int main(int argc, char *argv[])              bh[mi][i]=jl;       /* bias is positive if real duration
 {                                   * is higher than the multiple of stepm and negative otherwise.
                                    */
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;            }
   double agedeb, agefin,hf;            else{
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
   double fret;            }
   double **xi,tmp,delta;            if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
   double dum; /* Dummy variable */              bh[mi][i]=ju; /* At least one step */
   double ***p3mat;              /*  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);*/
   int *indx;            }
   char line[MAXLINE], linepar[MAXLINE];          } /* end if mle */
   char title[MAXLINE];        }
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      } /* end wave */
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    }
      jmean=sum/k;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    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);
     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);
   char filerest[FILENAMELENGTH];   }
   char fileregp[FILENAMELENGTH];  
   char popfile[FILENAMELENGTH];  /*********** Tricode ****************************/
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   int firstobs=1, lastobs=10;  {
   int sdeb, sfin; /* Status at beginning and end */    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   int c,  h , cpt,l;    /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
   int ju,jl, mi;    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    /* nbcode[Tvar[j]][1]= 
   int mobilav=0,popforecast=0;    */
   int hstepm, nhstepm;  
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
     int modmaxcovj=0; /* Modality max of covariates j */
   double bage, fage, age, agelim, agebase;    int cptcode=0; /* Modality max of covariates j */
   double ftolpl=FTOL;    int modmincovj=0; /* Modality min of covariates j */
   double **prlim;  
   double *severity;  
   double ***param; /* Matrix of parameters */    cptcoveff=0; 
   double  *p;   
   double **matcov; /* Matrix of covariance */    for (k=-1; k < maxncov; k++) Ndum[k]=0;
   double ***delti3; /* Scale */    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   double *delti; /* Scale */  
   double ***eij, ***vareij;    /* Loop on covariates without age and products */
   double **varpl; /* Variances of prevalence limits by age */    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
   double *epj, vepp;      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
   double kk1, kk2;                                 modality of this covariate Vj*/ 
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
                                        * If product of Vn*Vm, still boolean *:
                                       * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
   char version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
   char *alph[]={"a","a","b","c","d","e"}, str[4];        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                                         modality of the nth covariate of individual i. */
         if (ij > modmaxcovj)
   char z[1]="c", occ;          modmaxcovj=ij; 
 #include <sys/time.h>        else if (ij < modmincovj) 
 #include <time.h>          modmincovj=ij; 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        if ((ij < -1) && (ij > NCOVMAX)){
            printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
   /* long total_usecs;          exit(1);
   struct timeval start_time, end_time;        }else
          Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
   getcwd(pathcd, size);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         /* getting the maximum value of the modality of the covariate
   printf("\n%s",version);           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
   if(argc <=1){           female is 1, then modmaxcovj=1.*/
     printf("\nEnter the parameter file name: ");      }
     scanf("%s",pathtot);      printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
   }      cptcode=modmaxcovj;
   else{      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
     strcpy(pathtot,argv[1]);     /*for (i=0; i<=cptcode; i++) {*/
   }      for (i=modmincovj;  i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
   /*cygwin_split_path(pathtot,path,optionfile);        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
   /* cutv(path,optionfile,pathtot,'\\');*/        }
         /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);           historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      } /* Ndum[-1] number of undefined modalities */
   chdir(path);  
   replace(pathc,path);      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
       /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
 /*-------- arguments in the command line --------*/      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
          modmincovj=3; modmaxcovj = 7;
   strcpy(fileres,"r");         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
   strcat(fileres, optionfilefiname);         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
   strcat(fileres,".txt");    /* Other files have txt extension */         variables V1_1 and V1_2.
          nbcode[Tvar[j]][ij]=k;
   /*---------arguments file --------*/         nbcode[Tvar[j]][1]=0;
          nbcode[Tvar[j]][2]=1;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {         nbcode[Tvar[j]][3]=2;
     printf("Problem with optionfile %s\n",optionfile);      */
     goto end;      ij=1; /* ij is similar to i but can jumps over null modalities */
   }      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
         for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
   strcpy(filereso,"o");          /*recode from 0 */
   strcat(filereso,fileres);          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
   if((ficparo=fopen(filereso,"w"))==NULL) {            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;                                       k is a modality. If we have model=V1+V1*sex 
   }                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
             ij++;
   /* Reads comments: lines beginning with '#' */          }
   while((c=getc(ficpar))=='#' && c!= EOF){          if (ij > ncodemax[j]) break; 
     ungetc(c,ficpar);        }  /* end of loop on */
     fgets(line, MAXLINE, ficpar);      } /* end of loop on modality */ 
     puts(line);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
     fputs(line,ficparo);    
   }   for (k=-1; k< maxncov; k++) Ndum[k]=0; 
   ungetc(c,ficpar);    
     for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
   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);     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
   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);     Ndum[ij]++; 
 while((c=getc(ficpar))=='#' && c!= EOF){   } 
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);   ij=1;
     puts(line);   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
     fputs(line,ficparo);     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
   }     if((Ndum[i]!=0) && (i<=ncovcol)){
   ungetc(c,ficpar);       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
         Tvaraff[ij]=i; /*For printing (unclear) */
           ij++;
   covar=matrix(0,NCOVMAX,1,n);     }else
   cptcovn=0;         Tvaraff[ij]=0;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;   }
    ij--;
   ncovmodel=2+cptcovn;   cptcoveff=ij; /*Number of total covariates*/
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
    }
   /* Read guess parameters */  
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  /*********** Health Expectancies ****************/
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
     puts(line);  
     fputs(line,ficparo);  {
   }    /* Health expectancies, no variances */
   ungetc(c,ficpar);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
      int nhstepma, nstepma; /* Decreasing with age */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    double age, agelim, hf;
     for(i=1; i <=nlstate; i++)    double ***p3mat;
     for(j=1; j <=nlstate+ndeath-1; j++){    double eip;
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       fprintf(ficparo,"%1d%1d",i1,j1);    pstamp(ficreseij);
       printf("%1d%1d",i,j);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
       for(k=1; k<=ncovmodel;k++){    fprintf(ficreseij,"# Age");
         fscanf(ficpar," %lf",&param[i][j][k]);    for(i=1; i<=nlstate;i++){
         printf(" %lf",param[i][j][k]);      for(j=1; j<=nlstate;j++){
         fprintf(ficparo," %lf",param[i][j][k]);        fprintf(ficreseij," e%1d%1d ",i,j);
       }      }
       fscanf(ficpar,"\n");      fprintf(ficreseij," e%1d. ",i);
       printf("\n");    }
       fprintf(ficparo,"\n");    fprintf(ficreseij,"\n");
     }  
      
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   p=param[1][1];    }
      else  hstepm=estepm;   
   /* Reads comments: lines beginning with '#' */    /* We compute the life expectancy from trapezoids spaced every estepm months
   while((c=getc(ficpar))=='#' && c!= EOF){     * This is mainly to measure the difference between two models: for example
     ungetc(c,ficpar);     * if stepm=24 months pijx are given only every 2 years and by summing them
     fgets(line, MAXLINE, ficpar);     * we are calculating an estimate of the Life Expectancy assuming a linear 
     puts(line);     * progression in between and thus overestimating or underestimating according
     fputs(line,ficparo);     * to the curvature of the survival function. If, for the same date, we 
   }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   ungetc(c,ficpar);     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);     * curvature will be obtained if estepm is as small as stepm. */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  
   for(i=1; i <=nlstate; i++){    /* For example we decided to compute the life expectancy with the smallest unit */
     for(j=1; j <=nlstate+ndeath-1; j++){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       fscanf(ficpar,"%1d%1d",&i1,&j1);       nhstepm is the number of hstepm from age to agelim 
       printf("%1d%1d",i,j);       nstepm is the number of stepm from age to agelin. 
       fprintf(ficparo,"%1d%1d",i1,j1);       Look at hpijx to understand the reason of that which relies in memory size
       for(k=1; k<=ncovmodel;k++){       and note for a fixed period like estepm months */
         fscanf(ficpar,"%le",&delti3[i][j][k]);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         printf(" %le",delti3[i][j][k]);       survival function given by stepm (the optimization length). Unfortunately it
         fprintf(ficparo," %le",delti3[i][j][k]);       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 
       fscanf(ficpar,"\n");       results. So we changed our mind and took the option of the best precision.
       printf("\n");    */
       fprintf(ficparo,"\n");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     }  
   }    agelim=AGESUP;
   delti=delti3[1][1];    /* If stepm=6 months */
        /* Computed by stepm unit matrices, product of hstepm matrices, stored
   /* Reads comments: lines beginning with '#' */         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   while((c=getc(ficpar))=='#' && c!= EOF){      
     ungetc(c,ficpar);  /* nhstepm age range expressed in number of stepm */
     fgets(line, MAXLINE, ficpar);    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     puts(line);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     fputs(line,ficparo);    /* if (stepm >= YEARM) hstepm=1;*/
   }    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   ungetc(c,ficpar);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    
   matcov=matrix(1,npar,1,npar);    for (age=bage; age<=fage; age ++){ 
   for(i=1; i <=npar; i++){      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     fscanf(ficpar,"%s",&str);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     printf("%s",str);      /* if (stepm >= YEARM) hstepm=1;*/
     fprintf(ficparo,"%s",str);      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
     for(j=1; j <=i; j++){  
       fscanf(ficpar," %le",&matcov[i][j]);      /* If stepm=6 months */
       printf(" %.5le",matcov[i][j]);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
       fprintf(ficparo," %.5le",matcov[i][j]);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
     }      
     fscanf(ficpar,"\n");      hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     printf("\n");      
     fprintf(ficparo,"\n");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   }      
   for(i=1; i <=npar; i++)      printf("%d|",(int)age);fflush(stdout);
     for(j=i+1;j<=npar;j++)      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       matcov[i][j]=matcov[j][i];      
          /* Computing expectancies */
   printf("\n");      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     /*-------- Rewriting paramater file ----------*/            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
      strcpy(rfileres,"r");    /* "Rparameterfile */            
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/            /* 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]);*/
      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(ficreseij,"%3.0f",age );
     }      for(i=1; i<=nlstate;i++){
     fprintf(ficres,"#%s\n",version);        eip=0;
            for(j=1; j<=nlstate;j++){
     /*-------- data file ----------*/          eip +=eij[i][j][(int)age];
     if((fic=fopen(datafile,"r"))==NULL)    {          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
       printf("Problem with datafile: %s\n", datafile);goto end;        }
     }        fprintf(ficreseij,"%9.4f", eip );
       }
     n= lastobs;      fprintf(ficreseij,"\n");
     severity = vector(1,maxwav);      
     outcome=imatrix(1,maxwav+1,1,n);    }
     num=ivector(1,n);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     moisnais=vector(1,n);    printf("\n");
     annais=vector(1,n);    fprintf(ficlog,"\n");
     moisdc=vector(1,n);    
     andc=vector(1,n);  }
     agedc=vector(1,n);  
     cod=ivector(1,n);  void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
     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);    /* Covariances of health expectancies eij and of total life expectancies according
     anint=matrix(1,maxwav,1,n);     to initial status i, ei. .
     s=imatrix(1,maxwav+1,1,n);    */
     adl=imatrix(1,maxwav+1,1,n);        int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     tab=ivector(1,NCOVMAX);    int nhstepma, nstepma; /* Decreasing with age */
     ncodemax=ivector(1,8);    double age, agelim, hf;
     double ***p3matp, ***p3matm, ***varhe;
     i=1;    double **dnewm,**doldm;
     while (fgets(line, MAXLINE, fic) != NULL)    {    double *xp, *xm;
       if ((i >= firstobs) && (i <=lastobs)) {    double **gp, **gm;
            double ***gradg, ***trgradg;
         for (j=maxwav;j>=1;j--){    int theta;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  
           strcpy(line,stra);    double eip, vip;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
         }    xp=vector(1,npar);
            xm=vector(1,npar);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    dnewm=matrix(1,nlstate*nlstate,1,npar);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    pstamp(ficresstdeij);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     fprintf(ficresstdeij,"# Age");
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    for(i=1; i<=nlstate;i++){
         for (j=ncovcol;j>=1;j--){      for(j=1; j<=nlstate;j++)
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
         }      fprintf(ficresstdeij," e%1d. ",i);
         num[i]=atol(stra);    }
            fprintf(ficresstdeij,"\n");
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){  
           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;}*/    pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
         i=i+1;    fprintf(ficrescveij,"# Age");
       }    for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=nlstate;j++){
     /* printf("ii=%d", ij);        cptj= (j-1)*nlstate+i;
        scanf("%d",i);*/        for(i2=1; i2<=nlstate;i2++)
   imx=i-1; /* Number of individuals */          for(j2=1; j2<=nlstate;j2++){
             cptj2= (j2-1)*nlstate+i2;
   /* for (i=1; i<=imx; i++){            if(cptj2 <= cptj)
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          }
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      }
     }*/    fprintf(ficrescveij,"\n");
    /*  for (i=1; i<=imx; i++){    
      if (s[4][i]==9)  s[4][i]=-1;    if(estepm < stepm){
      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]));}*/      printf ("Problem %d lower than %d\n",estepm, stepm);
      }
      else  hstepm=estepm;   
   /* Calculation of the number of parameter from char model*/    /* We compute the life expectancy from trapezoids spaced every estepm months
   Tvar=ivector(1,15);     * This is mainly to measure the difference between two models: for example
   Tprod=ivector(1,15);     * if stepm=24 months pijx are given only every 2 years and by summing them
   Tvaraff=ivector(1,15);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   Tvard=imatrix(1,15,1,2);     * progression in between and thus overestimating or underestimating according
   Tage=ivector(1,15);           * to the curvature of the survival function. If, for the same date, we 
         * estimate the model with stepm=1 month, we can keep estepm to 24 months
   if (strlen(model) >1){     * to compare the new estimate of Life expectancy with the same linear 
     j=0, j1=0, k1=1, k2=1;     * hypothesis. A more precise result, taking into account a more precise
     j=nbocc(model,'+');     * curvature will be obtained if estepm is as small as stepm. */
     j1=nbocc(model,'*');  
     cptcovn=j+1;    /* For example we decided to compute the life expectancy with the smallest unit */
     cptcovprod=j1;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           nhstepm is the number of hstepm from age to agelim 
     strcpy(modelsav,model);       nstepm is the number of stepm from age to agelin. 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){       Look at hpijx to understand the reason of that which relies in memory size
       printf("Error. Non available option model=%s ",model);       and note for a fixed period like estepm months */
       goto end;    /* 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
           means that if the survival funtion is printed only each two years of age and if
     for(i=(j+1); i>=1;i--){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       cutv(stra,strb,modelsav,'+');       results. So we changed our mind and took the option of the best precision.
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       /*scanf("%d",i);*/  
       if (strchr(strb,'*')) {    /* If stepm=6 months */
         cutv(strd,strc,strb,'*');    /* nhstepm age range expressed in number of stepm */
         if (strcmp(strc,"age")==0) {    agelim=AGESUP;
           cptcovprod--;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
           cutv(strb,stre,strd,'V');    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           Tvar[i]=atoi(stre);    /* if (stepm >= YEARM) hstepm=1;*/
           cptcovage++;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
             Tage[cptcovage]=i;    
             /*printf("stre=%s ", stre);*/    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         else if (strcmp(strd,"age")==0) {    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
           cptcovprod--;    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
           cutv(strb,stre,strc,'V');    gp=matrix(0,nhstepm,1,nlstate*nlstate);
           Tvar[i]=atoi(stre);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
           cptcovage++;  
           Tage[cptcovage]=i;    for (age=bage; age<=fage; age ++){ 
         }      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
         else {      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           cutv(strb,stre,strc,'V');      /* if (stepm >= YEARM) hstepm=1;*/
           Tvar[i]=ncovcol+k1;      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
           cutv(strb,strc,strd,'V');  
           Tprod[k1]=i;      /* If stepm=6 months */
           Tvard[k1][1]=atoi(strc);      /* Computed by stepm unit matrices, product of hstepma matrices, stored
           Tvard[k1][2]=atoi(stre);         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           Tvar[cptcovn+k2]=Tvard[k1][1];      
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           for (k=1; k<=lastobs;k++)  
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      /* Computing  Variances of health expectancies */
           k1++;      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
           k2=k2+2;         decrease memory allocation */
         }      for(theta=1; theta <=npar; theta++){
       }        for(i=1; i<=npar; i++){ 
       else {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          xm[i] = x[i] - (i==theta ?delti[theta]:0);
        /*  scanf("%d",i);*/        }
       cutv(strd,strc,strb,'V');        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
       Tvar[i]=atoi(strc);        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
       }    
       strcpy(modelsav,stra);          for(j=1; j<= nlstate; j++){
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          for(i=1; i<=nlstate; i++){
         scanf("%d",i);*/            for(h=0; h<=nhstepm-1; h++){
     }              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.;
              }
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);          }
   printf("cptcovprod=%d ", cptcovprod);        }
   scanf("%d ",i);*/       
     fclose(fic);        for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
     /*  if(mle==1){*/            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
     if (weightopt != 1) { /* Maximisation without weights*/          }
       for(i=1;i<=n;i++) weight[i]=1.0;      }/* End theta */
     }      
     /*-calculation of age at interview from date of interview and age at death -*/      
     agev=matrix(1,maxwav,1,imx);      for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
     for (i=1; i<=imx; i++) {          for(theta=1; theta <=npar; theta++)
       for(m=2; (m<= maxwav); m++) {            trgradg[h][j][theta]=gradg[h][theta][j];
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      
          anint[m][i]=9999;  
          s[m][i]=-1;       for(ij=1;ij<=nlstate*nlstate;ij++)
        }        for(ji=1;ji<=nlstate*nlstate;ji++)
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;          varhe[ij][ji][(int)age] =0.;
       }  
     }       printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     for (i=1; i<=imx; i++)  {       for(h=0;h<=nhstepm-1;h++){
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        for(k=0;k<=nhstepm-1;k++){
       for(m=1; (m<= maxwav); m++){          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
         if(s[m][i] >0){          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           if (s[m][i] >= nlstate+1) {          for(ij=1;ij<=nlstate*nlstate;ij++)
             if(agedc[i]>0)            for(ji=1;ji<=nlstate*nlstate;ji++)
               if(moisdc[i]!=99 && andc[i]!=9999)              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
                 agev[m][i]=agedc[i];        }
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      }
            else {  
               if (andc[i]!=9999){      /* Computing expectancies */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
               agev[m][i]=-1;      for(i=1; i<=nlstate;i++)
               }        for(j=1; j<=nlstate;j++)
             }          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           }            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
           else if(s[m][i] !=9){ /* Should no more exist */            
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
             if(mint[m][i]==99 || anint[m][i]==9999)  
               agev[m][i]=1;          }
             else if(agev[m][i] <agemin){  
               agemin=agev[m][i];      fprintf(ficresstdeij,"%3.0f",age );
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      for(i=1; i<=nlstate;i++){
             }        eip=0.;
             else if(agev[m][i] >agemax){        vip=0.;
               agemax=agev[m][i];        for(j=1; j<=nlstate;j++){
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/          eip += eij[i][j][(int)age];
             }          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             /*agev[m][i]=anint[m][i]-annais[i];*/            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
             /*   agev[m][i] = age[i]+2*m;*/          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
           }        }
           else { /* =9 */        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
             agev[m][i]=1;      }
             s[m][i]=-1;      fprintf(ficresstdeij,"\n");
           }  
         }      fprintf(ficrescveij,"%3.0f",age );
         else /*= 0 Unknown */      for(i=1; i<=nlstate;i++)
           agev[m][i]=1;        for(j=1; j<=nlstate;j++){
       }          cptj= (j-1)*nlstate+i;
              for(i2=1; i2<=nlstate;i2++)
     }            for(j2=1; j2<=nlstate;j2++){
     for (i=1; i<=imx; i++)  {              cptj2= (j2-1)*nlstate+i2;
       for(m=1; (m<= maxwav); m++){              if(cptj2 <= cptj)
         if (s[m][i] > (nlstate+ndeath)) {                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
           printf("Error: Wrong value in nlstate or ndeath\n");              }
           goto end;        }
         }      fprintf(ficrescveij,"\n");
       }     
     }    }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_vector(severity,1,maxwav);    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_imatrix(outcome,1,maxwav+1,1,n);    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_vector(moisnais,1,n);    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_vector(annais,1,n);    printf("\n");
     /* free_matrix(mint,1,maxwav,1,n);    fprintf(ficlog,"\n");
        free_matrix(anint,1,maxwav,1,n);*/  
     free_vector(moisdc,1,n);    free_vector(xm,1,npar);
     free_vector(andc,1,n);    free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
        free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     wav=ivector(1,imx);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  }
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  
      /************ Variance ******************/
     /* Concatenates waves */  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[])
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       Tcode=ivector(1,100);    /* double **newm;*/
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    double **dnewm,**doldm;
       ncodemax[1]=1;    double **dnewmp,**doldmp;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    int i, j, nhstepm, hstepm, h, nstepm ;
          int k, cptcode;
    codtab=imatrix(1,100,1,10);    double *xp;
    h=0;    double **gp, **gm;  /* for var eij */
    m=pow(2,cptcoveff);    double ***gradg, ***trgradg; /*for var eij */
      double **gradgp, **trgradgp; /* for var p point j */
    for(k=1;k<=cptcoveff; k++){    double *gpp, *gmp; /* for var p point j */
      for(i=1; i <=(m/pow(2,k));i++){    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
        for(j=1; j <= ncodemax[k]; j++){    double ***p3mat;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    double age,agelim, hf;
            h++;    double ***mobaverage;
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    int theta;
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/    char digit[4];
          }    char digitp[25];
        }  
      }    char fileresprobmorprev[FILENAMELENGTH];
    }  
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    if(popbased==1){
       codtab[1][2]=1;codtab[2][2]=2; */      if(mobilav!=0)
    /* for(i=1; i <=m ;i++){        strcpy(digitp,"-populbased-mobilav-");
       for(k=1; k <=cptcovn; k++){      else strcpy(digitp,"-populbased-nomobil-");
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    }
       }    else 
       printf("\n");      strcpy(digitp,"-stablbased-");
       }  
       scanf("%d",i);*/    if (mobilav!=0) {
          mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    /* Calculates basic frequencies. Computes observed prevalence at single age      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
        and prints on file fileres'p'. */        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
          }
        }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    strcpy(fileresprobmorprev,"prmorprev"); 
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    sprintf(digit,"%-d",ij);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    strcat(fileresprobmorprev,digit); /* Tvar to be done */
          strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     /* For Powell, parameters are in a vector p[] starting at p[1]    strcat(fileresprobmorprev,fileres);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     if(mle==1){    }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     }   
        fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     /*--------- results files --------------*/    pstamp(ficresprobmorprev);
     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(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
      fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
    jk=1;      fprintf(ficresprobmorprev," p.%-d SE",j);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      for(i=1; i<=nlstate;i++)
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
    for(i=1,jk=1; i <=nlstate; i++){    }  
      for(k=1; k <=(nlstate+ndeath); k++){    fprintf(ficresprobmorprev,"\n");
        if (k != i)    fprintf(ficgp,"\n# Routine varevsij");
          {    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
            printf("%d%d ",i,k);    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(ficres,"%1d%1d ",i,k);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
            for(j=1; j <=ncovmodel; j++){  /*   } */
              printf("%f ",p[jk]);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
              fprintf(ficres,"%f ",p[jk]);    pstamp(ficresvij);
              jk++;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
            }    if(popbased==1)
            printf("\n");      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
            fprintf(ficres,"\n");    else
          }      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
      }    fprintf(ficresvij,"# Age");
    }    for(i=1; i<=nlstate;i++)
  if(mle==1){      for(j=1; j<=nlstate;j++)
     /* Computing hessian and covariance matrix */        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     ftolhess=ftol; /* Usually correct */    fprintf(ficresvij,"\n");
     hesscov(matcov, p, npar, delti, ftolhess, func);  
  }    xp=vector(1,npar);
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    dnewm=matrix(1,nlstate,1,npar);
     printf("# Scales (for hessian or gradient estimation)\n");    doldm=matrix(1,nlstate,1,nlstate);
      for(i=1,jk=1; i <=nlstate; i++){    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
       for(j=1; j <=nlstate+ndeath; j++){    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         if (j!=i) {  
           fprintf(ficres,"%1d%1d",i,j);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
           printf("%1d%1d",i,j);    gpp=vector(nlstate+1,nlstate+ndeath);
           for(k=1; k<=ncovmodel;k++){    gmp=vector(nlstate+1,nlstate+ndeath);
             printf(" %.5e",delti[jk]);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
             fprintf(ficres," %.5e",delti[jk]);    
             jk++;    if(estepm < stepm){
           }      printf ("Problem %d lower than %d\n",estepm, stepm);
           printf("\n");    }
           fprintf(ficres,"\n");    else  hstepm=estepm;   
         }    /* For example we decided to compute the life expectancy with the smallest unit */
       }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      }       nhstepm is the number of hstepm from age to agelim 
           nstepm is the number of stepm from age to agelin. 
     k=1;       Look at function hpijx to understand why (it is linked to memory size questions) */
     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");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     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");       survival function given by stepm (the optimization length). Unfortunately it
     for(i=1;i<=npar;i++){       means that if the survival funtion is printed every two years of age and if
       /*  if (k>nlstate) k=1;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       i1=(i-1)/(ncovmodel*nlstate)+1;       results. So we changed our mind and took the option of the best precision.
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    */
       printf("%s%d%d",alph[k],i1,tab[i]);*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       fprintf(ficres,"%3d",i);    agelim = AGESUP;
       printf("%3d",i);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       for(j=1; j<=i;j++){      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         fprintf(ficres," %.5e",matcov[i][j]);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         printf(" %.5e",matcov[i][j]);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       fprintf(ficres,"\n");      gp=matrix(0,nhstepm,1,nlstate);
       printf("\n");      gm=matrix(0,nhstepm,1,nlstate);
       k++;  
     }  
          for(theta=1; theta <=npar; theta++){
     while((c=getc(ficpar))=='#' && c!= EOF){        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
       ungetc(c,ficpar);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fgets(line, MAXLINE, ficpar);        }
       puts(line);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       fputs(line,ficparo);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     }  
     ungetc(c,ficpar);        if (popbased==1) {
     estepm=0;          if(mobilav ==0){
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);            for(i=1; i<=nlstate;i++)
     if (estepm==0 || estepm < stepm) estepm=stepm;              prlim[i][i]=probs[(int)age][i][ij];
     if (fage <= 2) {          }else{ /* mobilav */ 
       bage = ageminpar;            for(i=1; i<=nlstate;i++)
       fage = agemaxpar;              prlim[i][i]=mobaverage[(int)age][i][ij];
     }          }
            }
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);        for(j=1; j<= nlstate; j++){
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);          for(h=0; h<=nhstepm; h++){
              for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     while((c=getc(ficpar))=='#' && c!= EOF){              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);        }
     puts(line);        /* This for computing probability of death (h=1 means
     fputs(line,ficparo);           computed over hstepm matrices product = hstepm*stepm months) 
   }           as a weighted average of prlim.
   ungetc(c,ficpar);        */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        }    
              /* end probability of death */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     fgets(line, MAXLINE, ficpar);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     puts(line);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fputs(line,ficparo);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   }   
   ungetc(c,ficpar);        if (popbased==1) {
            if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
    dateprev1=anprev1+mprev1/12.+jprev1/365.;              prlim[i][i]=probs[(int)age][i][ij];
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
   fscanf(ficpar,"pop_based=%d\n",&popbased);              prlim[i][i]=mobaverage[(int)age][i][ij];
   fprintf(ficparo,"pop_based=%d\n",popbased);            }
   fprintf(ficres,"pop_based=%d\n",popbased);          }
    
   while((c=getc(ficpar))=='#' && c!= EOF){        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
     ungetc(c,ficpar);          for(h=0; h<=nhstepm; h++){
     fgets(line, MAXLINE, ficpar);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     puts(line);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     fputs(line,ficparo);          }
   }        }
   ungetc(c,ficpar);        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
   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);           as a weighted average of prlim.
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        */
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
 while((c=getc(ficpar))=='#' && c!= EOF){        }    
     ungetc(c,ficpar);        /* end probability of death */
     fgets(line, MAXLINE, ficpar);  
     puts(line);        for(j=1; j<= nlstate; j++) /* vareij */
     fputs(line,ficparo);          for(h=0; h<=nhstepm; h++){
   }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   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);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);        }
   
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      } /* End theta */
   
 /*------------ gnuplot -------------*/      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);  
        for(h=0; h<=nhstepm; h++) /* veij */
 /*------------ free_vector  -------------*/        for(j=1; j<=nlstate;j++)
  chdir(path);          for(theta=1; theta <=npar; theta++)
              trgradg[h][j][theta]=gradg[h][theta][j];
  free_ivector(wav,1,imx);  
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          for(theta=1; theta <=npar; theta++)
  free_ivector(num,1,n);          trgradgp[j][theta]=gradgp[theta][j];
  free_vector(agedc,1,n);    
  /*free_matrix(covar,1,NCOVMAX,1,n);*/  
  fclose(ficparo);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
  fclose(ficres);      for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
 /*--------- index.htm --------*/          vareij[i][j][(int)age] =0.;
   
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);      for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
            matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   /*--------------- Prevalence limit --------------*/          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
            for(i=1;i<=nlstate;i++)
   strcpy(filerespl,"pl");            for(j=1;j<=nlstate;j++)
   strcat(filerespl,fileres);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        }
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      }
   }    
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      /* pptj */
   fprintf(ficrespl,"#Prevalence limit\n");      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   fprintf(ficrespl,"#Age ");      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   fprintf(ficrespl,"\n");        for(i=nlstate+1;i<=nlstate+ndeath;i++)
            varppt[j][i]=doldmp[j][i];
   prlim=matrix(1,nlstate,1,nlstate);      /* end ppptj */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      /*  x centered again */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      if (popbased==1) {
   k=0;        if(mobilav ==0){
   agebase=ageminpar;          for(i=1; i<=nlstate;i++)
   agelim=agemaxpar;            prlim[i][i]=probs[(int)age][i][ij];
   ftolpl=1.e-10;        }else{ /* mobilav */ 
   i1=cptcoveff;          for(i=1; i<=nlstate;i++)
   if (cptcovn < 1){i1=1;}            prlim[i][i]=mobaverage[(int)age][i][ij];
         }
   for(cptcov=1;cptcov<=i1;cptcov++){      }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){               
         k=k+1;      /* This for computing probability of death (h=1 means
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         fprintf(ficrespl,"\n#******");         as a weighted average of prlim.
         for(j=1;j<=cptcoveff;j++)      */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         fprintf(ficrespl,"******\n");        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
                  gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
         for (age=agebase; age<=agelim; age++){      }    
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      /* end probability of death */
           fprintf(ficrespl,"%.0f",age );  
           for(i=1; i<=nlstate;i++)      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
           fprintf(ficrespl," %.5f", prlim[i][i]);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           fprintf(ficrespl,"\n");        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         }        for(i=1; i<=nlstate;i++){
       }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     }        }
   fclose(ficrespl);      } 
       fprintf(ficresprobmorprev,"\n");
   /*------------- h Pij x at various ages ------------*/  
        fprintf(ficresvij,"%.0f ",age );
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      for(i=1; i<=nlstate;i++)
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        for(j=1; j<=nlstate;j++){
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   }        }
   printf("Computing pij: result on file '%s' \n", filerespij);      fprintf(ficresvij,"\n");
        free_matrix(gp,0,nhstepm,1,nlstate);
   stepsize=(int) (stepm+YEARM-1)/YEARM;      free_matrix(gm,0,nhstepm,1,nlstate);
   /*if (stepm<=24) stepsize=2;*/      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   agelim=AGESUP;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   hstepm=stepsize*YEARM; /* Every year of age */    } /* End age */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    free_vector(gpp,nlstate+1,nlstate+ndeath);
      free_vector(gmp,nlstate+1,nlstate+ndeath);
   k=0;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   for(cptcov=1;cptcov<=i1;cptcov++){    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
       k=k+1;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
         fprintf(ficrespij,"\n#****** ");    fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
         for(j=1;j<=cptcoveff;j++)  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
         fprintf(ficrespij,"******\n");  /*   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));
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    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);
           oldm=oldms;savm=savms;    /*  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);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    */
           fprintf(ficrespij,"# Age");  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
           for(i=1; i<=nlstate;i++)    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %1d-%1d",i,j);    free_vector(xp,1,npar);
           fprintf(ficrespij,"\n");    free_matrix(doldm,1,nlstate,1,nlstate);
            for (h=0; h<=nhstepm; h++){    free_matrix(dnewm,1,nlstate,1,npar);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             for(i=1; i<=nlstate;i++)    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
               for(j=1; j<=nlstate+ndeath;j++)    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             fprintf(ficrespij,"\n");    fclose(ficresprobmorprev);
              }    fflush(ficgp);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fflush(fichtm); 
           fprintf(ficrespij,"\n");  }  /* 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[])
   {
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   fclose(ficrespij);    double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
   /*---------- Forecasting ------------------*/    int k, cptcode;
   if((stepm == 1) && (strcmp(model,".")==0)){    double *xp;
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    double *gp, *gm;
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    double **gradg, **trgradg;
   }    double age,agelim;
   else{    int theta;
     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);    pstamp(ficresvpl);
   }    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
      fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
   /*---------- Health expectancies and variances ------------*/        fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   strcpy(filerest,"t");  
   strcat(filerest,fileres);    xp=vector(1,npar);
   if((ficrest=fopen(filerest,"w"))==NULL) {    dnewm=matrix(1,nlstate,1,npar);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    doldm=matrix(1,nlstate,1,nlstate);
   }    
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
   strcpy(filerese,"e");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   strcat(filerese,fileres);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   if((ficreseij=fopen(filerese,"w"))==NULL) {      if (stepm >= YEARM) hstepm=1;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   }      gradg=matrix(1,npar,1,nlstate);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      gp=vector(1,nlstate);
       gm=vector(1,nlstate);
  strcpy(fileresv,"v");  
   strcat(fileresv,fileres);      for(theta=1; theta <=npar; theta++){
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        for(i=1; i<=npar; i++){ /* Computes gradient */
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   }        }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   calagedate=-1;        for(i=1;i<=nlstate;i++)
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          gp[i] = prlim[i][i];
       
   k=0;        for(i=1; i<=npar; i++) /* Computes gradient */
   for(cptcov=1;cptcov<=i1;cptcov++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       k=k+1;        for(i=1;i<=nlstate;i++)
       fprintf(ficrest,"\n#****** ");          gm[i] = prlim[i][i];
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(i=1;i<=nlstate;i++)
       fprintf(ficrest,"******\n");          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
       fprintf(ficreseij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)      trgradg =matrix(1,nlstate,1,npar);
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");      for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
       fprintf(ficresvij,"\n#****** ");          trgradg[j][theta]=gradg[theta][j];
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(i=1;i<=nlstate;i++)
       fprintf(ficresvij,"******\n");        varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       oldm=oldms;savm=savms;      for(i=1;i<=nlstate;i++)
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);          varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
    
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      fprintf(ficresvpl,"%.0f ",age );
       oldm=oldms;savm=savms;      for(i=1; i<=nlstate;i++)
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);        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);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      free_matrix(gradg,1,npar,1,nlstate);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      free_matrix(trgradg,1,nlstate,1,npar);
       fprintf(ficrest,"\n");    } /* End age */
   
       epj=vector(1,nlstate+1);    free_vector(xp,1,npar);
       for(age=bage; age <=fage ;age++){    free_matrix(doldm,1,nlstate,1,npar);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    free_matrix(dnewm,1,nlstate,1,nlstate);
         if (popbased==1) {  
           for(i=1; i<=nlstate;i++)  }
             prlim[i][i]=probs[(int)age][i][k];  
         }  /************ 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[])
         fprintf(ficrest," %4.0f",age);  {
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    int i, j=0,  i1, k1, l1, t, tj;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    int k2, l2, j1,  z1;
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    int k=0,l, cptcode;
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    int first=1, first1, first2;
           }    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
           epj[nlstate+1] +=epj[j];    double **dnewm,**doldm;
         }    double *xp;
     double *gp, *gm;
         for(i=1, vepp=0.;i <=nlstate;i++)    double **gradg, **trgradg;
           for(j=1;j <=nlstate;j++)    double **mu;
             vepp += vareij[i][j][(int)age];    double age,agelim, cov[NCOVMAX+1];
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
         for(j=1;j <=nlstate;j++){    int theta;
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    char fileresprob[FILENAMELENGTH];
         }    char fileresprobcov[FILENAMELENGTH];
         fprintf(ficrest,"\n");    char fileresprobcor[FILENAMELENGTH];
       }    double ***varpij;
     }  
   }    strcpy(fileresprob,"prob"); 
 free_matrix(mint,1,maxwav,1,n);    strcat(fileresprob,fileres);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
     free_vector(weight,1,n);      printf("Problem with resultfile: %s\n", fileresprob);
   fclose(ficreseij);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   fclose(ficresvij);    }
   fclose(ficrest);    strcpy(fileresprobcov,"probcov"); 
   fclose(ficpar);    strcat(fileresprobcov,fileres);
   free_vector(epj,1,nlstate+1);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobcov);
   /*------- Variance limit prevalence------*/        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
   strcpy(fileresvpl,"vpl");    strcpy(fileresprobcor,"probcor"); 
   strcat(fileresvpl,fileres);    strcat(fileresprobcor,fileres);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      printf("Problem with resultfile: %s\n", fileresprobcor);
     exit(0);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   }    }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    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);
   k=0;    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       k=k+1;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       fprintf(ficresvpl,"\n#****** ");    pstamp(ficresprob);
       for(j=1;j<=cptcoveff;j++)    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficresprob,"# Age");
       fprintf(ficresvpl,"******\n");    pstamp(ficresprobcov);
          fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    fprintf(ficresprobcov,"# Age");
       oldm=oldms;savm=savms;    pstamp(ficresprobcor);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     }    fprintf(ficresprobcor,"# Age");
  }  
   
   fclose(ficresvpl);    for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
   /*---------- End : free ----------------*/        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
          fprintf(ficresprobcor," p%1d-%1d ",i,j);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      }  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);   /* fprintf(ficresprob,"\n");
      fprintf(ficresprobcov,"\n");
      fprintf(ficresprobcor,"\n");
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);   */
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    xp=vector(1,npar);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   free_matrix(matcov,1,npar,1,npar);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   free_vector(delti,1,npar);    first=1;
   free_matrix(agev,1,maxwav,1,imx);    fprintf(ficgp,"\n# Routine varprob");
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   if(erreur >0)  
     printf("End of Imach with error or warning %d\n",erreur);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
   else   printf("End of Imach\n");    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    file %s<br>\n",optionfilehtmcov);
      fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   /* 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);*/  and drawn. It helps understanding how is the covariance between two incidences.\
   /*printf("Total time was %d uSec.\n", total_usecs);*/   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   /*------ End -----------*/    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 \
  end:  standard deviations wide on each axis. <br>\
 #ifdef windows   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
   /* chdir(pathcd);*/   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
 #endif  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
  /*system("wgnuplot graph.plt");*/  
  /*system("../gp37mgw/wgnuplot graph.plt");*/    cov[1]=1;
  /*system("cd ../gp37mgw");*/    /* tj=cptcoveff; */
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    tj = (int) pow(2,cptcoveff);
  strcpy(plotcmd,GNUPLOTPROGRAM);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
  strcat(plotcmd," ");    j1=0;
  strcat(plotcmd,optionfilegnuplot);    for(j1=1; j1<=tj;j1++){
  system(plotcmd);      /*for(i1=1; i1<=ncodemax[t];i1++){ */
       /*j1++;*/
 #ifdef windows        if  (cptcovn>0) {
   while (z[0] != 'q') {          fprintf(ficresprob, "\n#********** Variable "); 
     /* chdir(path); */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");          fprintf(ficresprob, "**********\n#\n");
     scanf("%s",z);          fprintf(ficresprobcov, "\n#********** Variable "); 
     if (z[0] == 'c') system("./imach");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     else if (z[0] == 'e') system(optionfilehtm);          fprintf(ficresprobcov, "**********\n#\n");
     else if (z[0] == 'g') system(plotcmd);          
     else if (z[0] == 'q') exit(0);          fprintf(ficgp, "\n#********** Variable "); 
   }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 #endif          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 with errno=%s\n",optionfile,strerror(errno));
       fprintf(ficlog,"Problem with optionfile %s with errno=%s\n",optionfile,strerror(errno));
       fflush(ficlog);
       /* goto end; */
       exit(70); 
     }
   
   
   
     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 command %s\n", plotcmd);
       printf("\n Trying on same directory\n");
       sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
       if((outcmd=system(plotcmd)) != 0)
         printf("\n Still a problem with gnuplot command %s\n", plotcmd);
     }
     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') {
   #ifdef OSX
         sprintf(pplotcmd, "open %s", optionfilehtm);
   #elsedef
         sprintf(pplotcmd, "%s", optionfilehtm);
   #enddef
         printf("Starting browser with: %s",plotcmd);fflush(stdout);
         system(plotcmd);
       }
       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.1.46  
changed lines
  Added in v.1.152


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