Diff for /imach/src/imach.c between versions 1.46 and 1.147

version 1.46, 2002/05/30 17:44:35 version 1.147, 2014/06/16 10:33:11
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.147  2014/06/16 10:33:11  brouard
      *** empty log message ***
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.146  2014/06/16 10:20:28  brouard
   first survey ("cross") where individuals from different ages are    Summary: Merge
   interviewed on their health status or degree of disability (in the    Author: Brouard
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Merge, before building revised version.
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.145  2014/06/10 21:23:15  brouard
   model. More health states you consider, more time is necessary to reach the    Summary: Debugging with valgrind
   Maximum Likelihood of the parameters involved in the model.  The    Author: Nicolas Brouard
   simplest model is the multinomial logistic model where pij is the  
   probability to be observed in state j at the second wave    Lot of changes in order to output the results with some covariates
   conditional to be observed in state i at the first wave. Therefore    After the Edimburgh REVES conference 2014, it seems mandatory to
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    improve the code.
   'age' is age and 'sex' is a covariate. If you want to have a more    No more memory valgrind error but a lot has to be done in order to
   complex model than "constant and age", you should modify the program    continue the work of splitting the code into subroutines.
   where the markup *Covariates have to be included here again* invites    Also, decodemodel has been improved. Tricode is still not
   you to do it.  More covariates you add, slower the    optimal. nbcode should be improved. Documentation has been added in
   convergence.    the source code.
   
   The advantage of this computer programme, compared to a simple    Revision 1.143  2014/01/26 09:45:38  brouard
   multinomial logistic model, is clear when the delay between waves is not    Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
   identical for each individual. Also, if a individual missed an  
   intermediate interview, the information is lost, but taken into    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   account using an interpolation or extrapolation.      (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
   
   hPijx is the probability to be observed in state i at age x+h    Revision 1.142  2014/01/26 03:57:36  brouard
   conditional to the observed state i at age x. The delay 'h' can be    Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.141  2014/01/26 02:42:01  brouard
   and the contribution of each individual to the likelihood is simply    * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
   hPijx.  
     Revision 1.140  2011/09/02 10:37:54  brouard
   Also this programme outputs the covariance matrix of the parameters but also    Summary: times.h is ok with mingw32 now.
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.139  2010/06/14 07:50:17  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
            Institut national d'études démographiques, Paris.    I remember having already fixed agemin agemax which are pointers now but not cvs saved.
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.138  2010/04/30 18:19:40  brouard
   It is copyrighted identically to a GNU software product, ie programme and    *** empty log message ***
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.137  2010/04/29 18:11:38  brouard
   **********************************************************************/    (Module): Checking covariates for more complex models
      than V1+V2. A lot of change to be done. Unstable.
 #include <math.h>  
 #include <stdio.h>    Revision 1.136  2010/04/26 20:30:53  brouard
 #include <stdlib.h>    (Module): merging some libgsl code. Fixing computation
 #include <unistd.h>    of likelione (using inter/intrapolation if mle = 0) in order to
     get same likelihood as if mle=1.
 #define MAXLINE 256    Some cleaning of code and comments added.
 #define GNUPLOTPROGRAM "gnuplot"  
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Revision 1.135  2009/10/29 15:33:14  brouard
 #define FILENAMELENGTH 80    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 /*#define DEBUG*/  
 #define windows    Revision 1.134  2009/10/29 13:18:53  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.133  2009/07/06 10:21:25  brouard
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    just nforces
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.132  2009/07/06 08:22:05  brouard
 #define NINTERVMAX 8    Many tings
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.131  2009/06/20 16:22:47  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    Some dimensions resccaled
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.130  2009/05/26 06:44:34  brouard
 #define AGESUP 130    (Module): Max Covariate is now set to 20 instead of 8. A
 #define AGEBASE 40    lot of cleaning with variables initialized to 0. Trying to make
     V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
   
 int erreur; /* Error number */    Revision 1.129  2007/08/31 13:49:27  lievre
 int nvar;    Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.128  2006/06/30 13:02:05  brouard
 int nlstate=2; /* Number of live states */    (Module): Clarifications on computing e.j
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.127  2006/04/28 18:11:50  brouard
 int popbased=0;    (Module): Yes the sum of survivors was wrong since
     imach-114 because nhstepm was no more computed in the age
 int *wav; /* Number of waves for this individuual 0 is possible */    loop. Now we define nhstepma in the age loop.
 int maxwav; /* Maxim number of waves */    (Module): In order to speed up (in case of numerous covariates) we
 int jmin, jmax; /* min, max spacing between 2 waves */    compute health expectancies (without variances) in a first step
 int mle, weightopt;    and then all the health expectancies with variances or standard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    deviation (needs data from the Hessian matrices) which slows the
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    computation.
 double jmean; /* Mean space between 2 waves */    In the future we should be able to stop the program is only health
 double **oldm, **newm, **savm; /* Working pointers to matrices */    expectancies and graph are needed without standard deviations.
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Revision 1.126  2006/04/28 17:23:28  brouard
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    (Module): Yes the sum of survivors was wrong since
 FILE *ficreseij;    imach-114 because nhstepm was no more computed in the age
   char filerese[FILENAMELENGTH];    loop. Now we define nhstepma in the age loop.
  FILE  *ficresvij;    Version 0.98h
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    Revision 1.125  2006/04/04 15:20:31  lievre
   char fileresvpl[FILENAMELENGTH];    Errors in calculation of health expectancies. Age was not initialized.
     Forecasting file added.
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.124  2006/03/22 17:13:53  lievre
 #define FTOL 1.0e-10    Parameters are printed with %lf instead of %f (more numbers after the comma).
     The log-likelihood is printed in the log file
 #define NRANSI  
 #define ITMAX 200    Revision 1.123  2006/03/20 10:52:43  brouard
     * imach.c (Module): <title> changed, corresponds to .htm file
 #define TOL 2.0e-4    name. <head> headers where missing.
   
 #define CGOLD 0.3819660    * imach.c (Module): Weights can have a decimal point as for
 #define ZEPS 1.0e-10    English (a comma might work with a correct LC_NUMERIC environment,
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    otherwise the weight is truncated).
     Modification of warning when the covariates values are not 0 or
 #define GOLD 1.618034    1.
 #define GLIMIT 100.0    Version 0.98g
 #define TINY 1.0e-20  
     Revision 1.122  2006/03/20 09:45:41  brouard
 static double maxarg1,maxarg2;    (Module): Weights can have a decimal point as for
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    English (a comma might work with a correct LC_NUMERIC environment,
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    otherwise the weight is truncated).
      Modification of warning when the covariates values are not 0 or
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    1.
 #define rint(a) floor(a+0.5)    Version 0.98g
   
 static double sqrarg;    Revision 1.121  2006/03/16 17:45:01  lievre
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    * imach.c (Module): Comments concerning covariates added
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     * imach.c (Module): refinements in the computation of lli if
 int imx;    status=-2 in order to have more reliable computation if stepm is
 int stepm;    not 1 month. Version 0.98f
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.120  2006/03/16 15:10:38  lievre
 int estepm;    (Module): refinements in the computation of lli if
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    status=-2 in order to have more reliable computation if stepm is
     not 1 month. Version 0.98f
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    Revision 1.119  2006/03/15 17:42:26  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    (Module): Bug if status = -2, the loglikelihood was
 double **pmmij, ***probs, ***mobaverage;    computed as likelihood omitting the logarithm. Version O.98e
 double dateintmean=0;  
     Revision 1.118  2006/03/14 18:20:07  brouard
 double *weight;    (Module): varevsij Comments added explaining the second
 int **s; /* Status */    table of variances if popbased=1 .
 double *agedc, **covar, idx;    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    (Module): Function pstamp added
     (Module): Version 0.98d
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.117  2006/03/14 17:16:22  brouard
     (Module): varevsij Comments added explaining the second
 /**************** split *************************/    table of variances if popbased=1 .
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 {    (Module): Function pstamp added
    char *s;                             /* pointer */    (Module): Version 0.98d
    int  l1, l2;                         /* length counters */  
     Revision 1.116  2006/03/06 10:29:27  brouard
    l1 = strlen( path );                 /* length of path */    (Module): Variance-covariance wrong links and
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    varian-covariance of ej. is needed (Saito).
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */    Revision 1.115  2006/02/27 12:17:45  brouard
 #else    (Module): One freematrix added in mlikeli! 0.98c
    s = strrchr( path, '/' );            /* find last / */  
 #endif    Revision 1.114  2006/02/26 12:57:58  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    (Module): Some improvements in processing parameter
 #if     defined(__bsd__)                /* get current working directory */    filename with strsep.
       extern char       *getwd( );  
     Revision 1.113  2006/02/24 14:20:24  brouard
       if ( getwd( dirc ) == NULL ) {    (Module): Memory leaks checks with valgrind and:
 #else    datafile was not closed, some imatrix were not freed and on matrix
       extern char       *getcwd( );    allocation too.
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.112  2006/01/30 09:55:26  brouard
 #endif    (Module): Back to gnuplot.exe instead of wgnuplot.exe
          return( GLOCK_ERROR_GETCWD );  
       }    Revision 1.111  2006/01/25 20:38:18  brouard
       strcpy( name, path );             /* we've got it */    (Module): Lots of cleaning and bugs added (Gompertz)
    } else {                             /* strip direcotry from path */    (Module): Comments can be added in data file. Missing date values
       s++;                              /* after this, the filename */    can be a simple dot '.'.
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.110  2006/01/25 00:51:50  brouard
       strcpy( name, s );                /* save file name */    (Module): Lots of cleaning and bugs added (Gompertz)
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.109  2006/01/24 19:37:15  brouard
    }    (Module): Comments (lines starting with a #) are allowed in data.
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows    Revision 1.108  2006/01/19 18:05:42  lievre
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Gnuplot problem appeared...
 #else    To be fixed
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif    Revision 1.107  2006/01/19 16:20:37  brouard
    s = strrchr( name, '.' );            /* find last / */    Test existence of gnuplot in imach path
    s++;  
    strcpy(ext,s);                       /* save extension */    Revision 1.106  2006/01/19 13:24:36  brouard
    l1= strlen( name);    Some cleaning and links added in html output
    l2= strlen( s)+1;  
    strncpy( finame, name, l1-l2);    Revision 1.105  2006/01/05 20:23:19  lievre
    finame[l1-l2]= 0;    *** empty log message ***
    return( 0 );                         /* we're done */  
 }    Revision 1.104  2005/09/30 16:11:43  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
 /******************************************/    that the person is alive, then we can code his/her status as -2
     (instead of missing=-1 in earlier versions) and his/her
 void replace(char *s, char*t)    contributions to the likelihood is 1 - Prob of dying from last
 {    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   int i;    the healthy state at last known wave). Version is 0.98
   int lg=20;  
   i=0;    Revision 1.103  2005/09/30 15:54:49  lievre
   lg=strlen(t);    (Module): sump fixed, loop imx fixed, and simplifications.
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Revision 1.102  2004/09/15 17:31:30  brouard
     if (t[i]== '\\') s[i]='/';    Add the possibility to read data file including tab characters.
   }  
 }    Revision 1.101  2004/09/15 10:38:38  brouard
     Fix on curr_time
 int nbocc(char *s, char occ)  
 {    Revision 1.100  2004/07/12 18:29:06  brouard
   int i,j=0;    Add version for Mac OS X. Just define UNIX in Makefile
   int lg=20;  
   i=0;    Revision 1.99  2004/06/05 08:57:40  brouard
   lg=strlen(s);    *** empty log message ***
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;    Revision 1.98  2004/05/16 15:05:56  brouard
   }    New version 0.97 . First attempt to estimate force of mortality
   return j;    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 .
     This is the basic analysis of mortality and should be done before any
 void cutv(char *u,char *v, char*t, char occ)    other analysis, in order to test if the mortality estimated from the
 {    cross-longitudinal survey is different from the mortality estimated
   int i,lg,j,p=0;    from other sources like vital statistic data.
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    The same imach parameter file can be used but the option for mle should be -3.
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    Agnès, who wrote this part of the code, tried to keep most of the
     former routines in order to include the new code within the former code.
   lg=strlen(t);  
   for(j=0; j<p; j++) {    The output is very simple: only an estimate of the intercept and of
     (u[j] = t[j]);    the slope with 95% confident intervals.
   }  
      u[p]='\0';    Current limitations:
     A) Even if you enter covariates, i.e. with the
    for(j=0; j<= lg; j++) {    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
     if (j>=(p+1))(v[j-p-1] = t[j]);    B) There is no computation of Life Expectancy nor Life Table.
   }  
 }    Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
 /********************** nrerror ********************/    suppressed.
   
 void nrerror(char error_text[])    Revision 1.96  2003/07/15 15:38:55  brouard
 {    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   fprintf(stderr,"ERREUR ...\n");    rewritten within the same printf. Workaround: many printfs.
   fprintf(stderr,"%s\n",error_text);  
   exit(1);    Revision 1.95  2003/07/08 07:54:34  brouard
 }    * imach.c (Repository):
 /*********************** vector *******************/    (Repository): Using imachwizard code to output a more meaningful covariance
 double *vector(int nl, int nh)    matrix (cov(a12,c31) instead of numbers.
 {  
   double *v;    Revision 1.94  2003/06/27 13:00:02  brouard
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Just cleaning
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    Revision 1.93  2003/06/25 16:33:55  brouard
 }    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 /************************ free vector ******************/    (Module): Version 0.96b
 void free_vector(double*v, int nl, int nh)  
 {    Revision 1.92  2003/06/25 16:30:45  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.
   
 /************************ivector *******************************/    Revision 1.91  2003/06/25 15:30:29  brouard
 int *ivector(long nl,long nh)    * imach.c (Repository): Duplicated warning errors corrected.
 {    (Repository): Elapsed time after each iteration is now output. It
   int *v;    helps to forecast when convergence will be reached. Elapsed time
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    is stamped in powell.  We created a new html file for the graphs
   if (!v) nrerror("allocation failure in ivector");    concerning matrix of covariance. It has extension -cov.htm.
   return v-nl+NR_END;  
 }    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
 /******************free ivector **************************/    mle=-1 a template is output in file "or"mypar.txt with the design
 void free_ivector(int *v, long nl, long nh)    of the covariance matrix to be input.
 {  
   free((FREE_ARG)(v+nl-NR_END));    Revision 1.89  2003/06/24 12:30:52  brouard
 }    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 /******************* imatrix *******************************/    of the covariance matrix to be input.
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    Revision 1.88  2003/06/23 17:54:56  brouard
 {    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;    Revision 1.87  2003/06/18 12:26:01  brouard
      Version 0.96
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    Revision 1.86  2003/06/17 20:04:08  brouard
   if (!m) nrerror("allocation failure 1 in matrix()");    (Module): Change position of html and gnuplot routines and added
   m += NR_END;    routine fileappend.
   m -= nrl;  
      Revision 1.85  2003/06/17 13:12:43  brouard
      * imach.c (Repository): Check when date of death was earlier that
   /* allocate rows and set pointers to them */    current date of interview. It may happen when the death was just
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    prior to the death. In this case, dh was negative and likelihood
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    was wrong (infinity). We still send an "Error" but patch by
   m[nrl] += NR_END;    assuming that the date of death was just one stepm after the
   m[nrl] -= ncl;    interview.
      (Repository): Because some people have very long ID (first column)
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    we changed int to long in num[] and we added a new lvector for
      memory allocation. But we also truncated to 8 characters (left
   /* return pointer to array of pointers to rows */    truncation)
   return m;    (Repository): No more line truncation errors.
 }  
     Revision 1.84  2003/06/13 21:44:43  brouard
 /****************** free_imatrix *************************/    * imach.c (Repository): Replace "freqsummary" at a correct
 void free_imatrix(m,nrl,nrh,ncl,nch)    place. It differs from routine "prevalence" which may be called
       int **m;    many times. Probs is memory consuming and must be used with
       long nch,ncl,nrh,nrl;    parcimony.
      /* free an int matrix allocated by imatrix() */    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    Revision 1.83  2003/06/10 13:39:11  lievre
   free((FREE_ARG) (m+nrl-NR_END));    *** empty log message ***
 }  
     Revision 1.82  2003/06/05 15:57:20  brouard
 /******************* matrix *******************************/    Add log in  imach.c and  fullversion number is now printed.
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {  */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  /*
   double **m;     Interpolated Markov Chain
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    Short summary of the programme:
   if (!m) nrerror("allocation failure 1 in matrix()");    
   m += NR_END;    This program computes Healthy Life Expectancies from
   m -= nrl;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    interviewed on their health status or degree of disability (in the
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    case of a health survey which is our main interest) -2- at least a
   m[nrl] += NR_END;    second wave of interviews ("longitudinal") which measure each change
   m[nrl] -= ncl;    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    model. More health states you consider, more time is necessary to reach the
   return m;    Maximum Likelihood of the parameters involved in the model.  The
 }    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
 /*************************free matrix ************************/    conditional to be observed in state i at the first wave. Therefore
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    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
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    complex model than "constant and age", you should modify the program
   free((FREE_ARG)(m+nrl-NR_END));    where the markup *Covariates have to be included here again* invites
 }    you to do it.  More covariates you add, slower the
     convergence.
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    The advantage of this computer programme, compared to a simple
 {    multinomial logistic model, is clear when the delay between waves is not
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    identical for each individual. Also, if a individual missed an
   double ***m;    intermediate interview, the information is lost, but taken into
     account using an interpolation or extrapolation.  
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");    hPijx is the probability to be observed in state i at age x+h
   m += NR_END;    conditional to the observed state i at age x. The delay 'h' can be
   m -= nrl;    split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    semester or year) is modelled as a multinomial logistic.  The hPx
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    matrix is simply the matrix product of nh*stepm elementary matrices
   m[nrl] += NR_END;    and the contribution of each individual to the likelihood is simply
   m[nrl] -= ncl;    hPijx.
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the period (stable) prevalence. 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   m[nrl][ncl] += NR_END;             Institut national d'études démographiques, Paris.
   m[nrl][ncl] -= nll;    This software have been partly granted by Euro-REVES, a concerted action
   for (j=ncl+1; j<=nch; j++)    from the European Union.
     m[nrl][j]=m[nrl][j-1]+nlay;    It is copyrighted identically to a GNU software product, ie programme and
      software can be distributed freely for non commercial use. Latest version
   for (i=nrl+1; i<=nrh; i++) {    can be accessed at http://euroreves.ined.fr/imach .
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
       m[i][j]=m[i][j-1]+nlay;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   }    
   return m;    **********************************************************************/
 }  /*
     main
 /*************************free ma3x ************************/    read parameterfile
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    read datafile
 {    concatwav
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    freqsummary
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    if (mle >= 1)
   free((FREE_ARG)(m+nrl-NR_END));      mlikeli
 }    print results files
     if mle==1 
 /***************** f1dim *************************/       computes hessian
 extern int ncom;    read end of parameter file: agemin, agemax, bage, fage, estepm
 extern double *pcom,*xicom;        begin-prev-date,...
 extern double (*nrfunc)(double []);    open gnuplot file
      open html file
 double f1dim(double x)    period (stable) prevalence      | pl_nom    1-1 2-2 etc by covariate
 {     for age prevalim()             | #****** V1=0  V2=1  V3=1  V4=0 ******
   int j;                                    | 65 1 0 2 1 3 1 4 0  0.96326 0.03674
   double f;      freexexit2 possible for memory heap.
   double *xt;  
      h Pij x                         | pij_nom  ficrestpij
   xt=vector(1,ncom);     # Cov Agex agex+h hpijx with i,j= 1-1 1-2     1-3     2-1     2-2     2-3
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];         1  85   85    1.00000             0.00000 0.00000 0.00000 1.00000 0.00000
   f=(*nrfunc)(xt);         1  85   86    0.68299             0.22291 0.09410 0.71093 0.00000 0.28907
   free_vector(xt,1,ncom);  
   return f;         1  65   99    0.00364             0.00322 0.99314 0.00350 0.00310 0.99340
 }         1  65  100    0.00214             0.00204 0.99581 0.00206 0.00196 0.99597
     variance of p one-step probabilities varprob  | prob_nom   ficresprob #One-step probabilities and stand. devi in ()
 /*****************brent *************************/     Standard deviation of one-step probabilities | probcor_nom   ficresprobcor #One-step probabilities and correlation matrix
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)     Matrix of variance covariance of one-step probabilities |  probcov_nom ficresprobcov #One-step probabilities and covariance matrix
 {  
   int iter;    forecasting if prevfcast==1 prevforecast call prevalence()
   double a,b,d,etemp;    health expectancies
   double fu,fv,fw,fx;    Variance-covariance of DFLE
   double ftemp;    prevalence()
   double p,q,r,tol1,tol2,u,v,w,x,xm;     movingaverage()
   double e=0.0;    varevsij() 
      if popbased==1 varevsij(,popbased)
   a=(ax < cx ? ax : cx);    total life expectancies
   b=(ax > cx ? ax : cx);    Variance of period (stable) prevalence
   x=w=v=bx;   end
   fw=fv=fx=(*f)(x);  */
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/   
     printf(".");fflush(stdout);  #include <math.h>
 #ifdef DEBUG  #include <stdio.h>
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  #include <stdlib.h>
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  #include <string.h>
 #endif  #include <unistd.h>
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  #include <limits.h>
       return fx;  #include <sys/types.h>
     }  #include <sys/stat.h>
     ftemp=fu;  #include <errno.h>
     if (fabs(e) > tol1) {  extern int errno;
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);  #ifdef LINUX
       p=(x-v)*q-(x-w)*r;  #include <time.h>
       q=2.0*(q-r);  #include "timeval.h"
       if (q > 0.0) p = -p;  #else
       q=fabs(q);  #include <sys/time.h>
       etemp=e;  #endif
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  #ifdef GSL
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  #include <gsl/gsl_errno.h>
       else {  #include <gsl/gsl_multimin.h>
         d=p/q;  #endif
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)  /* #include <libintl.h> */
           d=SIGN(tol1,xm-x);  /* #define _(String) gettext (String) */
       }  
     } else {  #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  #define GNUPLOTPROGRAM "gnuplot"
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
     fu=(*f)(u);  #define FILENAMELENGTH 132
     if (fu <= fx) {  
       if (u >= x) a=x; else b=x;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       SHFT(v,w,x,u)  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
         SHFT(fv,fw,fx,fu)  
         } else {  #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
           if (u < x) a=u; else b=u;  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
           if (fu <= fw || w == x) {  
             v=w;  #define NINTERVMAX 8
             w=u;  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
             fv=fw;  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
             fw=fu;  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
           } else if (fu <= fv || v == x || v == w) {  #define codtabm(h,k)  1 & (h-1) >> (k-1) ;
             v=u;  #define MAXN 20000
             fv=fu;  #define YEARM 12. /**< Number of months per year */
           }  #define AGESUP 130
         }  #define AGEBASE 40
   }  #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
   nrerror("Too many iterations in brent");  #ifdef UNIX
   *xmin=x;  #define DIRSEPARATOR '/'
   return fx;  #define CHARSEPARATOR "/"
 }  #define ODIRSEPARATOR '\\'
   #else
 /****************** mnbrak ***********************/  #define DIRSEPARATOR '\\'
   #define CHARSEPARATOR "\\"
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #define ODIRSEPARATOR '/'
             double (*func)(double))  #endif
 {  
   double ulim,u,r,q, dum;  /* $Id$ */
   double fu;  /* $State$ */
    
   *fa=(*func)(*ax);  char version[]="Imach version 0.98nR2, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
   *fb=(*func)(*bx);  char fullversion[]="$Revision$ $Date$"; 
   if (*fb > *fa) {  char strstart[80];
     SHFT(dum,*ax,*bx,dum)  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
       SHFT(dum,*fb,*fa,dum)  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
       }  int nvar=0, nforce=0; /* Number of variables, number of forces */
   *cx=(*bx)+GOLD*(*bx-*ax);  /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
   *fc=(*func)(*cx);  int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
   while (*fb > *fc) {  int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
     r=(*bx-*ax)*(*fb-*fc);  int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
     q=(*bx-*cx)*(*fb-*fa);  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  int cptcovprodnoage=0; /**< Number of covariate products without age */   
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  int cptcoveff=0; /* Total number of covariates to vary for printing results */
     ulim=(*bx)+GLIMIT*(*cx-*bx);  int cptcov=0; /* Working variable */
     if ((*bx-u)*(u-*cx) > 0.0) {  int npar=NPARMAX;
       fu=(*func)(u);  int nlstate=2; /* Number of live states */
     } else if ((*cx-u)*(u-ulim) > 0.0) {  int ndeath=1; /* Number of dead states */
       fu=(*func)(u);  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       if (fu < *fc) {  int popbased=0;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  int *wav; /* Number of waves for this individuual 0 is possible */
           }  int maxwav=0; /* Maxim number of waves */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
       u=ulim;  int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
       fu=(*func)(u);  int gipmx=0, gsw=0; /* Global variables on the number of contributions 
     } else {                     to the likelihood and the sum of weights (done by funcone)*/
       u=(*cx)+GOLD*(*cx-*bx);  int mle=1, weightopt=0;
       fu=(*func)(u);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
     }  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     SHFT(*ax,*bx,*cx,u)  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       SHFT(*fa,*fb,*fc,fu)             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       }  double jmean=1; /* Mean space between 2 waves */
 }  double **matprod2(); /* test */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
 /*************** linmin ************************/  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   /*FILE *fic ; */ /* Used in readdata only */
 int ncom;  FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 double *pcom,*xicom;  FILE *ficlog, *ficrespow;
 double (*nrfunc)(double []);  int globpr=0; /* Global variable for printing or not */
    double fretone; /* Only one call to likelihood */
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  long ipmx=0; /* Number of contributions */
 {  double sw; /* Sum of weights */
   double brent(double ax, double bx, double cx,  char filerespow[FILENAMELENGTH];
                double (*f)(double), double tol, double *xmin);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   double f1dim(double x);  FILE *ficresilk;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
               double *fc, double (*func)(double));  FILE *ficresprobmorprev;
   int j;  FILE *fichtm, *fichtmcov; /* Html File */
   double xx,xmin,bx,ax;  FILE *ficreseij;
   double fx,fb,fa;  char filerese[FILENAMELENGTH];
    FILE *ficresstdeij;
   ncom=n;  char fileresstde[FILENAMELENGTH];
   pcom=vector(1,n);  FILE *ficrescveij;
   xicom=vector(1,n);  char filerescve[FILENAMELENGTH];
   nrfunc=func;  FILE  *ficresvij;
   for (j=1;j<=n;j++) {  char fileresv[FILENAMELENGTH];
     pcom[j]=p[j];  FILE  *ficresvpl;
     xicom[j]=xi[j];  char fileresvpl[FILENAMELENGTH];
   }  char title[MAXLINE];
   ax=0.0;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   xx=1.0;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  char command[FILENAMELENGTH];
 #ifdef DEBUG  int  outcmd=0;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;  char filelog[FILENAMELENGTH]; /* Log file */
     p[j] += xi[j];  char filerest[FILENAMELENGTH];
   }  char fileregp[FILENAMELENGTH];
   free_vector(xicom,1,n);  char popfile[FILENAMELENGTH];
   free_vector(pcom,1,n);  
 }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
 /*************** powell ************************/  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  struct timezone tzp;
             double (*func)(double []))  extern int gettimeofday();
 {  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   void linmin(double p[], double xi[], int n, double *fret,  long time_value;
               double (*func)(double []));  extern long time();
   int i,ibig,j;  char strcurr[80], strfor[80];
   double del,t,*pt,*ptt,*xit;  
   double fp,fptt;  char *endptr;
   double *xits;  long lval;
   pt=vector(1,n);  double dval;
   ptt=vector(1,n);  
   xit=vector(1,n);  #define NR_END 1
   xits=vector(1,n);  #define FREE_ARG char*
   *fret=(*func)(p);  #define FTOL 1.0e-10
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  #define NRANSI 
     fp=(*fret);  #define ITMAX 200 
     ibig=0;  
     del=0.0;  #define TOL 2.0e-4 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     for (i=1;i<=n;i++)  #define CGOLD 0.3819660 
       printf(" %d %.12f",i, p[i]);  #define ZEPS 1.0e-10 
     printf("\n");  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  #define GOLD 1.618034 
       fptt=(*fret);  #define GLIMIT 100.0 
 #ifdef DEBUG  #define TINY 1.0e-20 
       printf("fret=%lf \n",*fret);  
 #endif  static double maxarg1,maxarg2;
       printf("%d",i);fflush(stdout);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       linmin(p,xit,n,fret,func);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       if (fabs(fptt-(*fret)) > del) {    
         del=fabs(fptt-(*fret));  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
         ibig=i;  #define rint(a) floor(a+0.5)
       }  
 #ifdef DEBUG  static double sqrarg;
       printf("%d %.12e",i,(*fret));  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       for (j=1;j<=n;j++) {  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  int agegomp= AGEGOMP;
         printf(" x(%d)=%.12e",j,xit[j]);  
       }  int imx; 
       for(j=1;j<=n;j++)  int stepm=1;
         printf(" p=%.12e",p[j]);  /* Stepm, step in month: minimum step interpolation*/
       printf("\n");  
 #endif  int estepm;
     }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  
 #ifdef DEBUG  int m,nb;
       int k[2],l;  long *num;
       k[0]=1;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       k[1]=-1;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       printf("Max: %.12e",(*func)(p));  double **pmmij, ***probs;
       for (j=1;j<=n;j++)  double *ageexmed,*agecens;
         printf(" %.12e",p[j]);  double dateintmean=0;
       printf("\n");  
       for(l=0;l<=1;l++) {  double *weight;
         for (j=1;j<=n;j++) {  int **s; /* Status */
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  double *agedc;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
         }                    * covar=matrix(0,NCOVMAX,1,n); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
       }  double  idx; 
 #endif  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   int *Ndum; /** Freq of modality (tricode */
   int **codtab; /**< codtab=imatrix(1,100,1,10); */
       free_vector(xit,1,n);  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
       free_vector(xits,1,n);  double *lsurv, *lpop, *tpop;
       free_vector(ptt,1,n);  
       free_vector(pt,1,n);  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
       return;  double ftolhess; /**< Tolerance for computing hessian */
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  /**************** split *************************/
     for (j=1;j<=n;j++) {  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       ptt[j]=2.0*p[j]-pt[j];  {
       xit[j]=p[j]-pt[j];    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       pt[j]=p[j];       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     }    */ 
     fptt=(*func)(ptt);    char  *ss;                            /* pointer */
     if (fptt < fp) {    int   l1, l2;                         /* length counters */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {    l1 = strlen(path );                   /* length of path */
         linmin(p,xit,n,fret,func);    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
         for (j=1;j<=n;j++) {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
           xi[j][ibig]=xi[j][n];    if ( ss == NULL ) {                   /* no directory, so determine current directory */
           xi[j][n]=xit[j];      strcpy( name, path );               /* we got the fullname name because no directory */
         }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 #ifdef DEBUG        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      /* get current working directory */
         for(j=1;j<=n;j++)      /*    extern  char* getcwd ( char *buf , int len);*/
           printf(" %.12e",xit[j]);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         printf("\n");        return( GLOCK_ERROR_GETCWD );
 #endif      }
       }      /* got dirc from getcwd*/
     }      printf(" DIRC = %s \n",dirc);
   }    } else {                              /* strip direcotry from path */
 }      ss++;                               /* after this, the filename */
       l2 = strlen( ss );                  /* length of filename */
 /**** Prevalence limit ****************/      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 {      dirc[l1-l2] = 0;                    /* add zero */
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      printf(" DIRC2 = %s \n",dirc);
      matrix by transitions matrix until convergence is reached */    }
     /* We add a separator at the end of dirc if not exists */
   int i, ii,j,k;    l1 = strlen( dirc );                  /* length of directory */
   double min, max, maxmin, maxmax,sumnew=0.;    if( dirc[l1-1] != DIRSEPARATOR ){
   double **matprod2();      dirc[l1] =  DIRSEPARATOR;
   double **out, cov[NCOVMAX], **pmij();      dirc[l1+1] = 0; 
   double **newm;      printf(" DIRC3 = %s \n",dirc);
   double agefin, delaymax=50 ; /* Max number of years to converge */    }
     ss = strrchr( name, '.' );            /* find last / */
   for (ii=1;ii<=nlstate+ndeath;ii++)    if (ss >0){
     for (j=1;j<=nlstate+ndeath;j++){      ss++;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      strcpy(ext,ss);                     /* save extension */
     }      l1= strlen( name);
       l2= strlen(ss)+1;
    cov[1]=1.;      strncpy( finame, name, l1-l2);
        finame[l1-l2]= 0;
  /* 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;    return( 0 );                          /* we're done */
     /* 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("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]]);*/  void replace_back_to_slash(char *s, char*t)
       }  {
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    int i;
       for (k=1; k<=cptcovprod;k++)    int lg=0;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    i=0;
     lg=strlen(t);
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    for(i=0; i<= lg; i++) {
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      (s[i] = t[i]);
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      if (t[i]== '\\') s[i]='/';
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    }
   }
     savm=oldm;  
     oldm=newm;  char *trimbb(char *out, char *in)
     maxmax=0.;  { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
     for(j=1;j<=nlstate;j++){    char *s;
       min=1.;    s=out;
       max=0.;    while (*in != '\0'){
       for(i=1; i<=nlstate; i++) {      while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
         sumnew=0;        in++;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      }
         prlim[i][j]= newm[i][j]/(1-sumnew);      *out++ = *in++;
         max=FMAX(max,prlim[i][j]);    }
         min=FMIN(min,prlim[i][j]);    *out='\0';
       }    return s;
       maxmin=max-min;  }
       maxmax=FMAX(maxmax,maxmin);  
     }  char *cutl(char *blocc, char *alocc, char *in, char occ)
     if(maxmax < ftolpl){  {
       return prlim;    /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ' 
     }       and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   }       gives blocc="abcdef2ghi" and alocc="j".
 }       If occ is not found blocc is null and alocc is equal to in. Returns blocc
     */
 /*************** transition probabilities ***************/    char *s, *t, *bl;
     t=in;s=in;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    while ((*in != occ) && (*in != '\0')){
 {      *alocc++ = *in++;
   double s1, s2;    }
   /*double t34;*/    if( *in == occ){
   int i,j,j1, nc, ii, jj;      *(alocc)='\0';
       s=++in;
     for(i=1; i<= nlstate; i++){    }
     for(j=1; j<i;j++){   
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    if (s == t) {/* occ not found */
         /*s2 += param[i][j][nc]*cov[nc];*/      *(alocc-(in-s))='\0';
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      in=s;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    }
       }    while ( *in != '\0'){
       ps[i][j]=s2;      *blocc++ = *in++;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    }
     }  
     for(j=i+1; j<=nlstate+ndeath;j++){    *blocc='\0';
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    return t;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  }
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  char *cutv(char *blocc, char *alocc, char *in, char occ)
       }  {
       ps[i][j]=s2;    /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ' 
     }       and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
   }       gives blocc="abcdef2ghi" and alocc="j".
     /*ps[3][2]=1;*/       If occ is not found blocc is null and alocc is equal to in. Returns alocc
     */
   for(i=1; i<= nlstate; i++){    char *s, *t;
      s1=0;    t=in;s=in;
     for(j=1; j<i; j++)    while (*in != '\0'){
       s1+=exp(ps[i][j]);      while( *in == occ){
     for(j=i+1; j<=nlstate+ndeath; j++)        *blocc++ = *in++;
       s1+=exp(ps[i][j]);        s=in;
     ps[i][i]=1./(s1+1.);      }
     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++)    if (s == t) /* occ not found */
       ps[i][j]= exp(ps[i][j])*ps[i][i];      *(blocc-(in-s))='\0';
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    else
   } /* end i */      *(blocc-(in-s)-1)='\0';
     in=s;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    while ( *in != '\0'){
     for(jj=1; jj<= nlstate+ndeath; jj++){      *alocc++ = *in++;
       ps[ii][jj]=0;    }
       ps[ii][ii]=1;  
     }    *alocc='\0';
   }    return s;
   }
   
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  int nbocc(char *s, char occ)
     for(jj=1; jj<= nlstate+ndeath; jj++){  {
      printf("%lf ",ps[ii][jj]);    int i,j=0;
    }    int lg=20;
     printf("\n ");    i=0;
     }    lg=strlen(s);
     printf("\n ");printf("%lf ",cov[2]);*/    for(i=0; i<= lg; i++) {
 /*    if  (s[i] == occ ) j++;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    }
   goto end;*/    return j;
     return ps;  }
 }  
   /* void cutv(char *u,char *v, char*t, char occ) */
 /**************** Product of 2 matrices ******************/  /* { */
   /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  /*      and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
 {  /*      gives u="abcdef2ghi" and v="j" *\/ */
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  /*   int i,lg,j,p=0; */
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  /*   i=0; */
   /* in, b, out are matrice of pointers which should have been initialized  /*   lg=strlen(t); */
      before: only the contents of out is modified. The function returns  /*   for(j=0; j<=lg-1; j++) { */
      a pointer to pointers identical to out */  /*     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
   long i, j, k;  /*   } */
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++)  /*   for(j=0; j<p; j++) { */
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  /*     (u[j] = t[j]); */
         out[i][k] +=in[i][j]*b[j][k];  /*   } */
   /*      u[p]='\0'; */
   return out;  
 }  /*    for(j=0; j<= lg; j++) { */
   /*     if (j>=(p+1))(v[j-p-1] = t[j]); */
   /*   } */
 /************* Higher Matrix Product ***************/  /* } */
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  /********************** nrerror ********************/
 {  
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  void nrerror(char error_text[])
      duration (i.e. until  {
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    fprintf(stderr,"ERREUR ...\n");
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    fprintf(stderr,"%s\n",error_text);
      (typically every 2 years instead of every month which is too big).    exit(EXIT_FAILURE);
      Model is determined by parameters x and covariates have to be  }
      included manually here.  /*********************** vector *******************/
   double *vector(int nl, int nh)
      */  {
     double *v;
   int i, j, d, h, k;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   double **out, cov[NCOVMAX];    if (!v) nrerror("allocation failure in vector");
   double **newm;    return v-nl+NR_END;
   }
   /* Hstepm could be zero and should return the unit matrix */  
   for (i=1;i<=nlstate+ndeath;i++)  /************************ free vector ******************/
     for (j=1;j<=nlstate+ndeath;j++){  void free_vector(double*v, int nl, int nh)
       oldm[i][j]=(i==j ? 1.0 : 0.0);  {
       po[i][j][0]=(i==j ? 1.0 : 0.0);    free((FREE_ARG)(v+nl-NR_END));
     }  }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
   for(h=1; h <=nhstepm; h++){  /************************ivector *******************************/
     for(d=1; d <=hstepm; d++){  int *ivector(long nl,long nh)
       newm=savm;  {
       /* Covariates have to be included here again */    int *v;
       cov[1]=1.;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    if (!v) nrerror("allocation failure in ivector");
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    return v-nl+NR_END;
       for (k=1; k<=cptcovage;k++)  }
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  /******************free ivector **************************/
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  void free_ivector(int *v, long nl, long nh)
   {
     free((FREE_ARG)(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]);*/  
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  /************************lvector *******************************/
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  long *lvector(long nl,long nh)
       savm=oldm;  {
       oldm=newm;    long *v;
     }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     for(i=1; i<=nlstate+ndeath; i++)    if (!v) nrerror("allocation failure in ivector");
       for(j=1;j<=nlstate+ndeath;j++) {    return v-nl+NR_END;
         po[i][j][h]=newm[i][j];  }
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  
          */  /******************free lvector **************************/
       }  void free_lvector(long *v, long nl, long nh)
   } /* end h */  {
   return po;    free((FREE_ARG)(v+nl-NR_END));
 }  }
   
   /******************* imatrix *******************************/
 /*************** log-likelihood *************/  int **imatrix(long nrl, long nrh, long ncl, long nch) 
 double func( double *x)       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 {  { 
   int i, ii, j, k, mi, d, kk;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    int **m; 
   double **out;    
   double sw; /* Sum of weights */    /* allocate pointers to rows */ 
   double lli; /* Individual log likelihood */    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   long ipmx;    if (!m) nrerror("allocation failure 1 in matrix()"); 
   /*extern weight */    m += NR_END; 
   /* We are differentiating ll according to initial status */    m -= nrl; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    
   /*for(i=1;i<imx;i++)    
     printf(" %d\n",s[4][i]);    /* allocate rows and set pointers to them */ 
   */    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   cov[1]=1.;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     m[nrl] += NR_END; 
   for(k=1; k<=nlstate; k++) ll[k]=0.;    m[nrl] -= ncl; 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     for(mi=1; mi<= wav[i]-1; mi++){    
       for (ii=1;ii<=nlstate+ndeath;ii++)    /* return pointer to array of pointers to rows */ 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    return m; 
       for(d=0; d<dh[mi][i]; d++){  } 
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  /****************** free_imatrix *************************/
         for (kk=1; kk<=cptcovage;kk++) {  void free_imatrix(m,nrl,nrh,ncl,nch)
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        int **m;
         }        long nch,ncl,nrh,nrl; 
               /* free an int matrix allocated by imatrix() */ 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  { 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         savm=oldm;    free((FREE_ARG) (m+nrl-NR_END)); 
         oldm=newm;  } 
          
          /******************* matrix *******************************/
       } /* end mult */  double **matrix(long nrl, long nrh, long ncl, long nch)
        {
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    double **m;
       ipmx +=1;  
       sw += weight[i];    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    if (!m) nrerror("allocation failure 1 in matrix()");
     } /* end of wave */    m += NR_END;
   } /* end of individual */    m -= nrl;
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    m[nrl] += NR_END;
   return -l;    m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
 /*********** Maximum Likelihood Estimation ***************/    /* 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
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
 {     */
   int i,j, iter;  }
   double **xi,*delti;  
   double fret;  /*************************free matrix ************************/
   xi=matrix(1,npar,1,npar);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   for (i=1;i<=npar;i++)  {
     for (j=1;j<=npar;j++)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       xi[i][j]=(i==j ? 1.0 : 0.0);    free((FREE_ARG)(m+nrl-NR_END));
   printf("Powell\n");  }
   powell(p,xi,npar,ftol,&iter,&fret,func);  
   /******************* ma3x *******************************/
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  {
     long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 }    double ***m;
   
 /**** Computes Hessian and covariance matrix ***/    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    if (!m) nrerror("allocation failure 1 in matrix()");
 {    m += NR_END;
   double  **a,**y,*x,pd;    m -= nrl;
   double **hess;  
   int i, j,jk;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   int *indx;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
   double hessii(double p[], double delta, int theta, double delti[]);    m[nrl] -= ncl;
   double hessij(double p[], double delti[], int i, int j);  
   void lubksb(double **a, int npar, int *indx, double b[]) ;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   void ludcmp(double **a, int npar, int *indx, double *d) ;  
     m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   hess=matrix(1,npar,1,npar);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     m[nrl][ncl] += NR_END;
   printf("\nCalculation of the hessian matrix. Wait...\n");    m[nrl][ncl] -= nll;
   for (i=1;i<=npar;i++){    for (j=ncl+1; j<=nch; j++) 
     printf("%d",i);fflush(stdout);      m[nrl][j]=m[nrl][j-1]+nlay;
     hess[i][i]=hessii(p,ftolhess,i,delti);    
     /*printf(" %f ",p[i]);*/    for (i=nrl+1; i<=nrh; i++) {
     /*printf(" %lf ",hess[i][i]);*/      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   }      for (j=ncl+1; j<=nch; j++) 
          m[i][j]=m[i][j-1]+nlay;
   for (i=1;i<=npar;i++) {    }
     for (j=1;j<=npar;j++)  {    return m; 
       if (j>i) {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         printf(".%d%d",i,j);fflush(stdout);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
         hess[i][j]=hessij(p,delti,i,j);    */
         hess[j][i]=hess[i][j];      }
         /*printf(" %lf ",hess[i][j]);*/  
       }  /*************************free ma3x ************************/
     }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   }  {
   printf("\n");    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    free((FREE_ARG)(m+nrl-NR_END));
    }
   a=matrix(1,npar,1,npar);  
   y=matrix(1,npar,1,npar);  /*************** function subdirf ***********/
   x=vector(1,npar);  char *subdirf(char fileres[])
   indx=ivector(1,npar);  {
   for (i=1;i<=npar;i++)    /* Caution optionfilefiname is hidden */
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    strcpy(tmpout,optionfilefiname);
   ludcmp(a,npar,indx,&pd);    strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
   for (j=1;j<=npar;j++) {    return tmpout;
     for (i=1;i<=npar;i++) x[i]=0;  }
     x[j]=1;  
     lubksb(a,npar,indx,x);  /*************** function subdirf2 ***********/
     for (i=1;i<=npar;i++){  char *subdirf2(char fileres[], char *preop)
       matcov[i][j]=x[i];  {
     }    
   }    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
   printf("\n#Hessian matrix#\n");    strcat(tmpout,"/");
   for (i=1;i<=npar;i++) {    strcat(tmpout,preop);
     for (j=1;j<=npar;j++) {    strcat(tmpout,fileres);
       printf("%.3e ",hess[i][j]);    return tmpout;
     }  }
     printf("\n");  
   }  /*************** function subdirf3 ***********/
   char *subdirf3(char fileres[], char *preop, char *preop2)
   /* Recompute Inverse */  {
   for (i=1;i<=npar;i++)    
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    /* Caution optionfilefiname is hidden */
   ludcmp(a,npar,indx,&pd);    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
   /*  printf("\n#Hessian matrix recomputed#\n");    strcat(tmpout,preop);
     strcat(tmpout,preop2);
   for (j=1;j<=npar;j++) {    strcat(tmpout,fileres);
     for (i=1;i<=npar;i++) x[i]=0;    return tmpout;
     x[j]=1;  }
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){  /***************** f1dim *************************/
       y[i][j]=x[i];  extern int ncom; 
       printf("%.3e ",y[i][j]);  extern double *pcom,*xicom;
     }  extern double (*nrfunc)(double []); 
     printf("\n");   
   }  double f1dim(double x) 
   */  { 
     int j; 
   free_matrix(a,1,npar,1,npar);    double f;
   free_matrix(y,1,npar,1,npar);    double *xt; 
   free_vector(x,1,npar);   
   free_ivector(indx,1,npar);    xt=vector(1,ncom); 
   free_matrix(hess,1,npar,1,npar);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
     free_vector(xt,1,ncom); 
 }    return f; 
   } 
 /*************** hessian matrix ****************/  
 double hessii( double x[], double delta, int theta, double delti[])  /*****************brent *************************/
 {  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   int i;  { 
   int l=1, lmax=20;    int iter; 
   double k1,k2;    double a,b,d,etemp;
   double p2[NPARMAX+1];    double fu,fv,fw,fx;
   double res;    double ftemp;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   double fx;    double e=0.0; 
   int k=0,kmax=10;   
   double l1;    a=(ax < cx ? ax : cx); 
     b=(ax > cx ? ax : cx); 
   fx=func(x);    x=w=v=bx; 
   for (i=1;i<=npar;i++) p2[i]=x[i];    fw=fv=fx=(*f)(x); 
   for(l=0 ; l <=lmax; l++){    for (iter=1;iter<=ITMAX;iter++) { 
     l1=pow(10,l);      xm=0.5*(a+b); 
     delts=delt;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     for(k=1 ; k <kmax; k=k+1){      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       delt = delta*(l1*k);      printf(".");fflush(stdout);
       p2[theta]=x[theta] +delt;      fprintf(ficlog,".");fflush(ficlog);
       k1=func(p2)-fx;  #ifdef DEBUG
       p2[theta]=x[theta]-delt;      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);
       k2=func(p2)-fx;      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);
       /*res= (k1-2.0*fx+k2)/delt/delt; */      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  #endif
            if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 #ifdef DEBUG        *xmin=x; 
       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);        return fx; 
 #endif      } 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      ftemp=fu;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      if (fabs(e) > tol1) { 
         k=kmax;        r=(x-w)*(fx-fv); 
       }        q=(x-v)*(fx-fw); 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        p=(x-v)*q-(x-w)*r; 
         k=kmax; l=lmax*10.;        q=2.0*(q-r); 
       }        if (q > 0.0) p = -p; 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        q=fabs(q); 
         delts=delt;        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)); 
   delti[theta]=delts;        else { 
   return res;          d=p/q; 
            u=x+d; 
 }          if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
 double hessij( double x[], double delti[], int thetai,int thetaj)        } 
 {      } else { 
   int i;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   int l=1, l1, lmax=20;      } 
   double k1,k2,k3,k4,res,fx;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double p2[NPARMAX+1];      fu=(*f)(u); 
   int k;      if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
   fx=func(x);        SHFT(v,w,x,u) 
   for (k=1; k<=2; k++) {          SHFT(fv,fw,fx,fu) 
     for (i=1;i<=npar;i++) p2[i]=x[i];          } else { 
     p2[thetai]=x[thetai]+delti[thetai]/k;            if (u < x) a=u; else b=u; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            if (fu <= fw || w == x) { 
     k1=func(p2)-fx;              v=w; 
                w=u; 
     p2[thetai]=x[thetai]+delti[thetai]/k;              fv=fw; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;              fw=fu; 
     k2=func(p2)-fx;            } else if (fu <= fv || v == x || v == w) { 
                v=u; 
     p2[thetai]=x[thetai]-delti[thetai]/k;              fv=fu; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            } 
     k3=func(p2)-fx;          } 
      } 
     p2[thetai]=x[thetai]-delti[thetai]/k;    nrerror("Too many iterations in brent"); 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    *xmin=x; 
     k4=func(p2)-fx;    return fx; 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  } 
 #ifdef DEBUG  
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  /****************** mnbrak ***********************/
 #endif  
   }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   return res;              double (*func)(double)) 
 }  { 
     double ulim,u,r,q, dum;
 /************** Inverse of matrix **************/    double fu; 
 void ludcmp(double **a, int n, int *indx, double *d)   
 {    *fa=(*func)(*ax); 
   int i,imax,j,k;    *fb=(*func)(*bx); 
   double big,dum,sum,temp;    if (*fb > *fa) { 
   double *vv;      SHFT(dum,*ax,*bx,dum) 
          SHFT(dum,*fb,*fa,dum) 
   vv=vector(1,n);        } 
   *d=1.0;    *cx=(*bx)+GOLD*(*bx-*ax); 
   for (i=1;i<=n;i++) {    *fc=(*func)(*cx); 
     big=0.0;    while (*fb > *fc) { 
     for (j=1;j<=n;j++)      r=(*bx-*ax)*(*fb-*fc); 
       if ((temp=fabs(a[i][j])) > big) big=temp;      q=(*bx-*cx)*(*fb-*fa); 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     vv[i]=1.0/big;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   }      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   for (j=1;j<=n;j++) {      if ((*bx-u)*(u-*cx) > 0.0) { 
     for (i=1;i<j;i++) {        fu=(*func)(u); 
       sum=a[i][j];      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        fu=(*func)(u); 
       a[i][j]=sum;        if (fu < *fc) { 
     }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     big=0.0;            SHFT(*fb,*fc,fu,(*func)(u)) 
     for (i=j;i<=n;i++) {            } 
       sum=a[i][j];      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       for (k=1;k<j;k++)        u=ulim; 
         sum -= a[i][k]*a[k][j];        fu=(*func)(u); 
       a[i][j]=sum;      } else { 
       if ( (dum=vv[i]*fabs(sum)) >= big) {        u=(*cx)+GOLD*(*cx-*bx); 
         big=dum;        fu=(*func)(u); 
         imax=i;      } 
       }      SHFT(*ax,*bx,*cx,u) 
     }        SHFT(*fa,*fb,*fc,fu) 
     if (j != imax) {        } 
       for (k=1;k<=n;k++) {  } 
         dum=a[imax][k];  
         a[imax][k]=a[j][k];  /*************** linmin ************************/
         a[j][k]=dum;  
       }  int ncom; 
       *d = -(*d);  double *pcom,*xicom;
       vv[imax]=vv[j];  double (*nrfunc)(double []); 
     }   
     indx[j]=imax;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     if (a[j][j] == 0.0) a[j][j]=TINY;  { 
     if (j != n) {    double brent(double ax, double bx, double cx, 
       dum=1.0/(a[j][j]);                 double (*f)(double), double tol, double *xmin); 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    double f1dim(double x); 
     }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   }                double *fc, double (*func)(double)); 
   free_vector(vv,1,n);  /* Doesn't work */    int j; 
 ;    double xx,xmin,bx,ax; 
 }    double fx,fb,fa;
    
 void lubksb(double **a, int n, int *indx, double b[])    ncom=n; 
 {    pcom=vector(1,n); 
   int i,ii=0,ip,j;    xicom=vector(1,n); 
   double sum;    nrfunc=func; 
      for (j=1;j<=n;j++) { 
   for (i=1;i<=n;i++) {      pcom[j]=p[j]; 
     ip=indx[i];      xicom[j]=xi[j]; 
     sum=b[ip];    } 
     b[ip]=b[i];    ax=0.0; 
     if (ii)    xx=1.0; 
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     else if (sum) ii=i;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     b[i]=sum;  #ifdef DEBUG
   }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   for (i=n;i>=1;i--) {    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     sum=b[i];  #endif
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    for (j=1;j<=n;j++) { 
     b[i]=sum/a[i][i];      xi[j] *= xmin; 
   }      p[j] += xi[j]; 
 }    } 
     free_vector(xicom,1,n); 
 /************ Frequencies ********************/    free_vector(pcom,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)  } 
 {  /* Some frequencies */  
    char *asc_diff_time(long time_sec, char ascdiff[])
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  {
   double ***freq; /* Frequencies */    long sec_left, days, hours, minutes;
   double *pp;    days = (time_sec) / (60*60*24);
   double pos, k2, dateintsum=0,k2cpt=0;    sec_left = (time_sec) % (60*60*24);
   FILE *ficresp;    hours = (sec_left) / (60*60) ;
   char fileresp[FILENAMELENGTH];    sec_left = (sec_left) %(60*60);
      minutes = (sec_left) /60;
   pp=vector(1,nlstate);    sec_left = (sec_left) % (60);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
   strcpy(fileresp,"p");    return ascdiff;
   strcat(fileresp,fileres);  }
   if((ficresp=fopen(fileresp,"w"))==NULL) {  
     printf("Problem with prevalence resultfile: %s\n", fileresp);  /*************** powell ************************/
     exit(0);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   }              double (*func)(double [])) 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  { 
   j1=0;    void linmin(double p[], double xi[], int n, double *fret, 
                  double (*func)(double [])); 
   j=cptcoveff;    int i,ibig,j; 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    double del,t,*pt,*ptt,*xit;
      double fp,fptt;
   for(k1=1; k1<=j;k1++){    double *xits;
     for(i1=1; i1<=ncodemax[k1];i1++){    int niterf, itmp;
       j1++;  
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    pt=vector(1,n); 
         scanf("%d", i);*/    ptt=vector(1,n); 
       for (i=-1; i<=nlstate+ndeath; i++)      xit=vector(1,n); 
         for (jk=-1; jk<=nlstate+ndeath; jk++)      xits=vector(1,n); 
           for(m=agemin; m <= agemax+3; m++)    *fret=(*func)(p); 
             freq[i][jk][m]=0;    for (j=1;j<=n;j++) pt[j]=p[j]; 
          for (*iter=1;;++(*iter)) { 
       dateintsum=0;      fp=(*fret); 
       k2cpt=0;      ibig=0; 
       for (i=1; i<=imx; i++) {      del=0.0; 
         bool=1;      last_time=curr_time;
         if  (cptcovn>0) {      (void) gettimeofday(&curr_time,&tzp);
           for (z1=1; z1<=cptcoveff; z1++)      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);
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      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);
               bool=0;  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
         }     for (i=1;i<=n;i++) {
         if (bool==1) {        printf(" %d %.12f",i, p[i]);
           for(m=firstpass; m<=lastpass; m++){        fprintf(ficlog," %d %.12lf",i, p[i]);
             k2=anint[m][i]+(mint[m][i]/12.);        fprintf(ficrespow," %.12lf", p[i]);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      }
               if(agev[m][i]==0) agev[m][i]=agemax+1;      printf("\n");
               if(agev[m][i]==1) agev[m][i]=agemax+2;      fprintf(ficlog,"\n");
               if (m<lastpass) {      fprintf(ficrespow,"\n");fflush(ficrespow);
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      if(*iter <=3){
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        tm = *localtime(&curr_time.tv_sec);
               }        strcpy(strcurr,asctime(&tm));
                /*       asctime_r(&tm,strcurr); */
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        forecast_time=curr_time; 
                 dateintsum=dateintsum+k2;        itmp = strlen(strcurr);
                 k2cpt++;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
               }          strcurr[itmp-1]='\0';
             }        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
           }        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         }        for(niterf=10;niterf<=30;niterf+=10){
       }          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
                  tmf = *localtime(&forecast_time.tv_sec);
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  /*      asctime_r(&tmf,strfor); */
           strcpy(strfor,asctime(&tmf));
       if  (cptcovn>0) {          itmp = strlen(strfor);
         fprintf(ficresp, "\n#********** Variable ");          if(strfor[itmp-1]=='\n')
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          strfor[itmp-1]='\0';
         fprintf(ficresp, "**********\n#");          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       }          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       for(i=1; i<=nlstate;i++)        }
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      }
       fprintf(ficresp, "\n");      for (i=1;i<=n;i++) { 
              for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       for(i=(int)agemin; i <= (int)agemax+3; i++){        fptt=(*fret); 
         if(i==(int)agemax+3)  #ifdef DEBUG
           printf("Total");        printf("fret=%lf \n",*fret);
         else        fprintf(ficlog,"fret=%lf \n",*fret);
           printf("Age %d", i);  #endif
         for(jk=1; jk <=nlstate ; jk++){        printf("%d",i);fflush(stdout);
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        fprintf(ficlog,"%d",i);fflush(ficlog);
             pp[jk] += freq[jk][m][i];        linmin(p,xit,n,fret,func); 
         }        if (fabs(fptt-(*fret)) > del) { 
         for(jk=1; jk <=nlstate ; jk++){          del=fabs(fptt-(*fret)); 
           for(m=-1, pos=0; m <=0 ; m++)          ibig=i; 
             pos += freq[jk][m][i];        } 
           if(pp[jk]>=1.e-10)  #ifdef DEBUG
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        printf("%d %.12e",i,(*fret));
           else        fprintf(ficlog,"%d %.12e",i,(*fret));
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        for (j=1;j<=n;j++) {
         }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           printf(" x(%d)=%.12e",j,xit[j]);
         for(jk=1; jk <=nlstate ; jk++){          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        }
             pp[jk] += freq[jk][m][i];        for(j=1;j<=n;j++) {
         }          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
         for(jk=1,pos=0; jk <=nlstate ; jk++)        }
           pos += pp[jk];        printf("\n");
         for(jk=1; jk <=nlstate ; jk++){        fprintf(ficlog,"\n");
           if(pos>=1.e-5)  #endif
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      } 
           else      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  #ifdef DEBUG
           if( i <= (int) agemax){        int k[2],l;
             if(pos>=1.e-5){        k[0]=1;
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        k[1]=-1;
               probs[i][jk][j1]= pp[jk]/pos;        printf("Max: %.12e",(*func)(p));
               /*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,"Max: %.12e",(*func)(p));
             }        for (j=1;j<=n;j++) {
             else          printf(" %.12e",p[j]);
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          fprintf(ficlog," %.12e",p[j]);
           }        }
         }        printf("\n");
                fprintf(ficlog,"\n");
         for(jk=-1; jk <=nlstate+ndeath; jk++)        for(l=0;l<=1;l++) {
           for(m=-1; m <=nlstate+ndeath; m++)          for (j=1;j<=n;j++) {
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         if(i <= (int) agemax)            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           fprintf(ficresp,"\n");            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         printf("\n");          }
       }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   }        }
   dateintmean=dateintsum/k2cpt;  #endif
    
   fclose(ficresp);  
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        free_vector(xit,1,n); 
   free_vector(pp,1,nlstate);        free_vector(xits,1,n); 
          free_vector(ptt,1,n); 
   /* End of Freq */        free_vector(pt,1,n); 
 }        return; 
       } 
 /************ Prevalence ********************/      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 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)      for (j=1;j<=n;j++) { 
 {  /* Some frequencies */        ptt[j]=2.0*p[j]-pt[j]; 
          xit[j]=p[j]-pt[j]; 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        pt[j]=p[j]; 
   double ***freq; /* Frequencies */      } 
   double *pp;      fptt=(*func)(ptt); 
   double pos, k2;      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   pp=vector(1,nlstate);        if (t < 0.0) { 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          linmin(p,xit,n,fret,func); 
            for (j=1;j<=n;j++) { 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            xi[j][ibig]=xi[j][n]; 
   j1=0;            xi[j][n]=xit[j]; 
            }
   j=cptcoveff;  #ifdef DEBUG
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
            fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   for(k1=1; k1<=j;k1++){          for(j=1;j<=n;j++){
     for(i1=1; i1<=ncodemax[k1];i1++){            printf(" %.12e",xit[j]);
       j1++;            fprintf(ficlog," %.12e",xit[j]);
                }
       for (i=-1; i<=nlstate+ndeath; i++)            printf("\n");
         for (jk=-1; jk<=nlstate+ndeath; jk++)            fprintf(ficlog,"\n");
           for(m=agemin; m <= agemax+3; m++)  #endif
             freq[i][jk][m]=0;        }
            } 
       for (i=1; i<=imx; i++) {    } 
         bool=1;  } 
         if  (cptcovn>0) {  
           for (z1=1; z1<=cptcoveff; z1++)  /**** Prevalence limit (stable or period prevalence)  ****************/
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  
               bool=0;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         }  {
         if (bool==1) {    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
           for(m=firstpass; m<=lastpass; m++){       matrix by transitions matrix until convergence is reached */
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    int i, ii,j,k;
               if(agev[m][i]==0) agev[m][i]=agemax+1;    double min, max, maxmin, maxmax,sumnew=0.;
               if(agev[m][i]==1) agev[m][i]=agemax+2;    /* double **matprod2(); */ /* test */
               if (m<lastpass) {    double **out, cov[NCOVMAX+1], **pmij();
                 if (calagedate>0)    double **newm;
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    double agefin, delaymax=50 ; /* Max number of years to converge */
                 else  
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    for (ii=1;ii<=nlstate+ndeath;ii++)
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];      for (j=1;j<=nlstate+ndeath;j++){
               }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             }      }
           }  
         }     cov[1]=1.;
       }   
       for(i=(int)agemin; i <= (int)agemax+3; i++){   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
         for(jk=1; jk <=nlstate ; jk++){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      newm=savm;
             pp[jk] += freq[jk][m][i];      /* Covariates have to be included here again */
         }      cov[2]=agefin;
         for(jk=1; jk <=nlstate ; jk++){      
           for(m=-1, pos=0; m <=0 ; m++)      for (k=1; k<=cptcovn;k++) {
             pos += freq[jk][m][i];        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]]);*/
              }
         for(jk=1; jk <=nlstate ; jk++){      /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
             pp[jk] += freq[jk][m][i];      /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
         }      
              /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      /*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]);*/
         for(jk=1; jk <=nlstate ; jk++){          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
           if( i <= (int) agemax){      /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
             if(pos>=1.e-5){      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
               probs[i][jk][j1]= pp[jk]/pos;      
             }      savm=oldm;
           }      oldm=newm;
         }      maxmax=0.;
              for(j=1;j<=nlstate;j++){
       }        min=1.;
     }        max=0.;
   }        for(i=1; i<=nlstate; i++) {
           sumnew=0;
            for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          prlim[i][j]= newm[i][j]/(1-sumnew);
   free_vector(pp,1,nlstate);          /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
            max=FMAX(max,prlim[i][j]);
 }  /* End of Freq */          min=FMIN(min,prlim[i][j]);
         }
 /************* Waves Concatenation ***************/        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      }
 {      if(maxmax < ftolpl){
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        return prlim;
      Death is a valid wave (if date is known).      }
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    }
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  }
      and mw[mi+1][i]. dh depends on stepm.  
      */  /*************** transition probabilities ***************/ 
   
   int i, mi, m;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  {
      double sum=0., jmean=0.;*/    /* According to parameters values stored in x and the covariate's values stored in cov,
        computes the probability to be observed in state j being in state i by appying the
   int j, k=0,jk, ju, jl;       model to the ncovmodel covariates (including constant and age).
   double sum=0.;       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
   jmin=1e+5;       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
   jmax=-1;       ncth covariate in the global vector x is given by the formula:
   jmean=0.;       j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
   for(i=1; i<=imx; i++){       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
     mi=0;       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
     m=firstpass;       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
     while(s[m][i] <= nlstate){       Outputs ps[i][j] the probability to be observed in j being in j according to
       if(s[m][i]>=1)       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
         mw[++mi][i]=m;    */
       if(m >=lastpass)    double s1, lnpijopii;
         break;    /*double t34;*/
       else    int i,j,j1, nc, ii, jj;
         m++;  
     }/* end while */      for(i=1; i<= nlstate; i++){
     if (s[m][i] > nlstate){        for(j=1; j<i;j++){
       mi++;     /* Death is another wave */          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
       /* if(mi==0)  never been interviewed correctly before death */            /*lnpijopii += param[i][j][nc]*cov[nc];*/
          /* Only death is a correct wave */            lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
       mw[mi][i]=m;  /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     }          }
           ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
     wav[i]=mi;  /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
     if(mi==0)        }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        for(j=i+1; j<=nlstate+ndeath;j++){
   }          for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
             /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
   for(i=1; i<=imx; i++){            lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
     for(mi=1; mi<wav[i];mi++){  /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
       if (stepm <=0)          }
         dh[mi][i]=1;          ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       else{        }
         if (s[mw[mi+1][i]][i] > nlstate) {      }
           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 */        s1=0;
           k=k+1;        for(j=1; j<i; j++){
           if (j >= jmax) jmax=j;          s1+=exp(ps[i][j]); /* In fact sums pij/pii */
           if (j <= jmin) jmin=j;          /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
           sum=sum+j;        }
           /*if (j<0) printf("j=%d num=%d \n",j,i); */        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); */
         else{        }
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
           k=k+1;        ps[i][i]=1./(s1+1.);
           if (j >= jmax) jmax=j;        /* Computing other pijs */
           else if (j <= jmin)jmin=j;        for(j=1; j<i; j++)
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          ps[i][j]= exp(ps[i][j])*ps[i][i];
           sum=sum+j;        for(j=i+1; j<=nlstate+ndeath; j++)
         }          ps[i][j]= exp(ps[i][j])*ps[i][i];
         jk= j/stepm;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         jl= j -jk*stepm;      } /* end i */
         ju= j -(jk+1)*stepm;      
         if(jl <= -ju)      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
           dh[mi][i]=jk;        for(jj=1; jj<= nlstate+ndeath; jj++){
         else          ps[ii][jj]=0;
           dh[mi][i]=jk+1;          ps[ii][ii]=1;
         if(dh[mi][i]==0)        }
           dh[mi][i]=1; /* At least one step */      }
       }      
     }      
   }      /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
   jmean=sum/k;      /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      /*  printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
  }      /*   } */
 /*********** Tricode ****************************/      /*   printf("\n "); */
 void tricode(int *Tvar, int **nbcode, int imx)      /* } */
 {      /* printf("\n ");printf("%lf ",cov[2]);*/
   int Ndum[20],ij=1, k, j, i;      /*
   int cptcode=0;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
   cptcoveff=0;        goto end;*/
        return ps;
   for (k=0; k<19; k++) Ndum[k]=0;  }
   for (k=1; k<=7; k++) ncodemax[k]=0;  
   /**************** Product of 2 matrices ******************/
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  
     for (i=1; i<=imx; i++) {  double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
       ij=(int)(covar[Tvar[j]][i]);  {
       Ndum[ij]++;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       if (ij > cptcode) cptcode=ij;    /* in, b, out are matrice of pointers which should have been initialized 
     }       before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
     for (i=0; i<=cptcode; i++) {    int i, j, k;
       if(Ndum[i]!=0) ncodemax[j]++;    for(i=nrl; i<= nrh; i++)
     }      for(k=ncolol; k<=ncoloh; k++){
     ij=1;        out[i][k]=0.;
         for(j=ncl; j<=nch; j++)
           out[i][k] +=in[i][j]*b[j][k];
     for (i=1; i<=ncodemax[j]; i++) {      }
       for (k=0; k<=19; k++) {    return out;
         if (Ndum[k] != 0) {  }
           nbcode[Tvar[j]][ij]=k;  
            
           ij++;  /************* Higher Matrix Product ***************/
         }  
         if (ij > ncodemax[j]) break;  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 
   }         'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
  for (k=0; k<19; k++) Ndum[k]=0;       nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
  for (i=1; i<=ncovmodel-2; i++) {       (typically every 2 years instead of every month which is too big 
       ij=Tvar[i];       for the memory).
       Ndum[ij]++;       Model is determined by parameters x and covariates have to be 
     }       included manually here. 
   
  ij=1;       */
  for (i=1; i<=10; i++) {  
    if((Ndum[i]!=0) && (i<=ncovcol)){    int i, j, d, h, k;
      Tvaraff[ij]=i;    double **out, cov[NCOVMAX+1];
      ij++;    double **newm;
    }  
  }    /* Hstepm could be zero and should return the unit matrix */
      for (i=1;i<=nlstate+ndeath;i++)
     cptcoveff=ij-1;      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);
 /*********** Health Expectancies ****************/      }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 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 )    for(h=1; h <=nhstepm; h++){
       for(d=1; d <=hstepm; d++){
 {        newm=savm;
   /* Health expectancies */        /* Covariates have to be included here again */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;        cov[1]=1.;
   double age, agelim, hf;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   double ***p3mat,***varhe;        for (k=1; k<=cptcovn;k++) 
   double **dnewm,**doldm;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double *xp;        for (k=1; k<=cptcovage;k++)
   double **gp, **gm;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double ***gradg, ***trgradg;        for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
   int theta;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);  
   xp=vector(1,npar);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   dnewm=matrix(1,nlstate*2,1,npar);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   doldm=matrix(1,nlstate*2,1,nlstate*2);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                       pmij(pmmij,cov,ncovmodel,x,nlstate));
   fprintf(ficreseij,"# Health expectancies\n");        savm=oldm;
   fprintf(ficreseij,"# Age");        oldm=newm;
   for(i=1; i<=nlstate;i++)      }
     for(j=1; j<=nlstate;j++)      for(i=1; i<=nlstate+ndeath; i++)
       fprintf(ficreseij," %1d-%1d (SE)",i,j);        for(j=1;j<=nlstate+ndeath;j++) {
   fprintf(ficreseij,"\n");          po[i][j][h]=newm[i][j];
           /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
   if(estepm < stepm){        }
     printf ("Problem %d lower than %d\n",estepm, stepm);      /*printf("h=%d ",h);*/
   }    } /* end h */
   else  hstepm=estepm;    /*     printf("\n H=%d \n",h); */
   /* We compute the life expectancy from trapezoids spaced every estepm months    return po;
    * This is mainly to measure the difference between two models: for example  }
    * if stepm=24 months pijx are given only every 2 years and by summing them  
    * we are calculating an estimate of the Life Expectancy assuming a linear  
    * progression inbetween and thus overestimating or underestimating according  /*************** log-likelihood *************/
    * to the curvature of the survival function. If, for the same date, we  double func( double *x)
    * estimate the model with stepm=1 month, we can keep estepm to 24 months  {
    * to compare the new estimate of Life expectancy with the same linear    int i, ii, j, k, mi, d, kk;
    * hypothesis. A more precise result, taking into account a more precise    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
    * curvature will be obtained if estepm is as small as stepm. */    double **out;
     double sw; /* Sum of weights */
   /* For example we decided to compute the life expectancy with the smallest unit */    double lli; /* Individual log likelihood */
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    int s1, s2;
      nhstepm is the number of hstepm from age to agelim    double bbh, survp;
      nstepm is the number of stepm from age to agelin.    long ipmx;
      Look at hpijx to understand the reason of that which relies in memory size    /*extern weight */
      and note for a fixed period like estepm months */    /* We are differentiating ll according to initial status */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      survival function given by stepm (the optimization length). Unfortunately it    /*for(i=1;i<imx;i++) 
      means that if the survival funtion is printed only each two years of age and if      printf(" %d\n",s[4][i]);
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    */
      results. So we changed our mind and took the option of the best precision.    cov[1]=1.;
   */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
   agelim=AGESUP;    if(mle==1){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     /* nhstepm age range expressed in number of stepm */        /* Computes the values of the ncovmodel covariates of the model
     nstepm=(int) rint((agelim-age)*YEARM/stepm);           depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
     /* if (stepm >= YEARM) hstepm=1;*/           to be observed in j being in i according to the model.
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */         */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);          cov[2+k]=covar[Tvar[k]][i];
     gp=matrix(0,nhstepm,1,nlstate*2);        }
     gm=matrix(0,nhstepm,1,nlstate*2);        /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
            is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored           has been calculated etc */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        for(mi=1; mi<= wav[i]-1; mi++){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
     /* Computing Variances of health expectancies */          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
      for(theta=1; theta <=npar; theta++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(i=1; i<=npar; i++){            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]; /* Tage[kk] gives the data-covariate associated with age */
       }            }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       cptj=0;            savm=oldm;
       for(j=1; j<= nlstate; j++){            oldm=newm;
         for(i=1; i<=nlstate; i++){          } /* end mult */
           cptj=cptj+1;        
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;          /* But now since version 0.9 we anticipate for bias at large stepm.
           }           * 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
                 * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
       for(i=1; i<=npar; i++)           * probability in order to take into account the bias as a fraction of the way
         xp[i] = x[i] - (i==theta ?delti[theta]:0);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);             * -stepm/2 to stepm/2 .
                 * For stepm=1 the results are the same as for previous versions of Imach.
       cptj=0;           * For stepm > 1 the results are less biased than in previous versions. 
       for(j=1; j<= nlstate; j++){           */
         for(i=1;i<=nlstate;i++){          s1=s[mw[mi][i]][i];
           cptj=cptj+1;          s2=s[mw[mi+1][i]][i];
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){          bbh=(double)bh[mi][i]/(double)stepm; 
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;          /* bias bh is positive if real duration
           }           * is higher than the multiple of stepm and negative otherwise.
         }           */
       }          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       for(j=1; j<= nlstate*2; j++)          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 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];               then the contribution to the likelihood is the probability to 
         }               die between last step unit time and current  step unit time, 
      }               which is also equal to probability to die before dh 
                   minus probability to die before dh-stepm . 
 /* End theta */               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);          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
      for(h=0; h<=nhstepm-1; h++)          to consider that at each interview the state was recorded
       for(j=1; j<=nlstate*2;j++)          (healthy, disable or death) and IMaCh was corrected; but when we
         for(theta=1; theta <=npar; theta++)          introduced the exact date of death then we should have modified
           trgradg[h][j][theta]=gradg[h][theta][j];          the contribution of an exact death to the likelihood. This new
                contribution is smaller and very dependent of the step unit
           stepm. It is no more the probability to die between last interview
      for(i=1;i<=nlstate*2;i++)          and month of death but the probability to survive from last
       for(j=1;j<=nlstate*2;j++)          interview up to one month before death multiplied by the
         varhe[i][j][(int)age] =0.;          probability to die within a month. Thanks to Chris
           Jackson for correcting this bug.  Former versions increased
      printf("%d|",(int)age);fflush(stdout);          mortality artificially. The bad side is that we add another loop
      for(h=0;h<=nhstepm-1;h++){          which slows down the processing. The difference can be up to 10%
       for(k=0;k<=nhstepm-1;k++){          lower mortality.
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);            */
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);            lli=log(out[s1][s2] - savm[s1][s2]);
         for(i=1;i<=nlstate*2;i++)  
           for(j=1;j<=nlstate*2;j++)  
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;          } else if  (s2==-2) {
       }            for (j=1,survp=0. ; j<=nlstate; j++) 
     }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             /*survp += out[s1][j]; */
                  lli= log(survp);
     /* Computing expectancies */          }
     for(i=1; i<=nlstate;i++)          
       for(j=1; j<=nlstate;j++)          else if  (s2==-4) { 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){            for (j=3,survp=0. ; j<=nlstate; j++)  
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                      lli= log(survp); 
 /* 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]);*/          } 
   
         }          else if  (s2==-5) { 
             for (j=1,survp=0. ; j<=2; j++)  
     fprintf(ficreseij,"%3.0f",age );              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     cptj=0;            lli= log(survp); 
     for(i=1; i<=nlstate;i++)          } 
       for(j=1; j<=nlstate;j++){          
         cptj++;          else{
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
     fprintf(ficreseij,"\n");          } 
              /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     free_matrix(gm,0,nhstepm,1,nlstate*2);          /*if(lli ==000.0)*/
     free_matrix(gp,0,nhstepm,1,nlstate*2);          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);          ipmx +=1;
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          sw += weight[i];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        } /* end of wave */
   free_vector(xp,1,npar);      } /* end of individual */
   free_matrix(dnewm,1,nlstate*2,1,npar);    }  else if(mle==2){
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 }        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
 /************ Variance ******************/            for (j=1;j<=nlstate+ndeath;j++){
 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)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* Variance of health expectancies */            }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          for(d=0; d<=dh[mi][i]; d++){
   double **newm;            newm=savm;
   double **dnewm,**doldm;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int i, j, nhstepm, hstepm, h, nstepm ;            for (kk=1; kk<=cptcovage;kk++) {
   int k, cptcode;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double *xp;            }
   double **gp, **gm;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double ***gradg, ***trgradg;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double ***p3mat;            savm=oldm;
   double age,agelim, hf;            oldm=newm;
   int theta;          } /* end mult */
         
   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");          s1=s[mw[mi][i]][i];
   fprintf(ficresvij,"# Age");          s2=s[mw[mi+1][i]][i];
   for(i=1; i<=nlstate;i++)          bbh=(double)bh[mi][i]/(double)stepm; 
     for(j=1; j<=nlstate;j++)          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          ipmx +=1;
   fprintf(ficresvij,"\n");          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   xp=vector(1,npar);        } /* end of wave */
   dnewm=matrix(1,nlstate,1,npar);      } /* end of individual */
   doldm=matrix(1,nlstate,1,nlstate);    }  else if(mle==3){  /* exponential inter-extrapolation */
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   if(estepm < stepm){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     printf ("Problem %d lower than %d\n",estepm, stepm);        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
   else  hstepm=estepm;              for (j=1;j<=nlstate+ndeath;j++){
   /* For example we decided to compute the life expectancy with the smallest unit */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.              savm[ii][j]=(ii==j ? 1.0 : 0.0);
      nhstepm is the number of hstepm from age to agelim            }
      nstepm is the number of stepm from age to agelin.          for(d=0; d<dh[mi][i]; d++){
      Look at hpijx to understand the reason of that which relies in memory size            newm=savm;
      and note for a fixed period like k years */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the            for (kk=1; kk<=cptcovage;kk++) {
      survival function given by stepm (the optimization length). Unfortunately it              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      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            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      results. So we changed our mind and took the option of the best precision.                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   */            savm=oldm;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */            oldm=newm;
   agelim = AGESUP;          } /* end mult */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          s1=s[mw[mi][i]][i];
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          s2=s[mw[mi+1][i]][i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          bbh=(double)bh[mi][i]/(double)stepm; 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          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 */
     gp=matrix(0,nhstepm,1,nlstate);          ipmx +=1;
     gm=matrix(0,nhstepm,1,nlstate);          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(theta=1; theta <=npar; theta++){        } /* end of wave */
       for(i=1; i<=npar; i++){ /* Computes gradient */      } /* end of individual */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
       if (popbased==1) {            for (j=1;j<=nlstate+ndeath;j++){
         for(i=1; i<=nlstate;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           prlim[i][i]=probs[(int)age][i][ij];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
            for(d=0; d<dh[mi][i]; d++){
       for(j=1; j<= nlstate; j++){            newm=savm;
         for(h=0; h<=nhstepm; h++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            for (kk=1; kk<=cptcovage;kk++) {
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }            }
       }          
                out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(i=1; i<=npar; i++) /* Computes gradient */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            savm=oldm;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              oldm=newm;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          } /* end mult */
          
       if (popbased==1) {          s1=s[mw[mi][i]][i];
         for(i=1; i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
           prlim[i][i]=probs[(int)age][i][ij];          if( s2 > nlstate){ 
       }            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
       for(j=1; j<= nlstate; j++){            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         for(h=0; h<=nhstepm; h++){          }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          ipmx +=1;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          sw += weight[i];
         }          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]); */
         } /* end of wave */
       for(j=1; j<= nlstate; j++)      } /* end of individual */
         for(h=0; h<=nhstepm; h++){    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     } /* End theta */        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(h=0; h<=nhstepm; h++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<=nlstate;j++)            }
         for(theta=1; theta <=npar; theta++)          for(d=0; d<dh[mi][i]; d++){
           trgradg[h][j][theta]=gradg[h][theta][j];            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */            for (kk=1; kk<=cptcovage;kk++) {
     for(i=1;i<=nlstate;i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(j=1;j<=nlstate;j++)            }
         vareij[i][j][(int)age] =0.;          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for(h=0;h<=nhstepm;h++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(k=0;k<=nhstepm;k++){            savm=oldm;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);            oldm=newm;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          } /* end mult */
         for(i=1;i<=nlstate;i++)        
           for(j=1;j<=nlstate;j++)          s1=s[mw[mi][i]][i];
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;          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;
           sw += weight[i];
     fprintf(ficresvij,"%.0f ",age );          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(i=1; i<=nlstate;i++)          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
       for(j=1; j<=nlstate;j++){        } /* end of wave */
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);      } /* end of individual */
       }    } /* End of if */
     fprintf(ficresvij,"\n");    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     free_matrix(gp,0,nhstepm,1,nlstate);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     free_matrix(gm,0,nhstepm,1,nlstate);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    return -l;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */  /*************** log-likelihood *************/
    double funcone( double *x)
   free_vector(xp,1,npar);  {
   free_matrix(doldm,1,nlstate,1,npar);    /* Same as likeli but slower because of a lot of printf and if */
   free_matrix(dnewm,1,nlstate,1,nlstate);    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
 }    double **out;
     double lli; /* Individual log likelihood */
 /************ Variance of prevlim ******************/    double llt;
 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)    int s1, s2;
 {    double bbh, survp;
   /* Variance of prevalence limit */    /*extern weight */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /* We are differentiating ll according to initial status */
   double **newm;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   double **dnewm,**doldm;    /*for(i=1;i<imx;i++) 
   int i, j, nhstepm, hstepm;      printf(" %d\n",s[4][i]);
   int k, cptcode;    */
   double *xp;    cov[1]=1.;
   double *gp, *gm;  
   double **gradg, **trgradg;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   double age,agelim;  
   int theta;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");      for(mi=1; mi<= wav[i]-1; mi++){
   fprintf(ficresvpl,"# Age");        for (ii=1;ii<=nlstate+ndeath;ii++)
   for(i=1; i<=nlstate;i++)          for (j=1;j<=nlstate+ndeath;j++){
       fprintf(ficresvpl," %1d-%1d",i,i);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficresvpl,"\n");            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
   xp=vector(1,npar);        for(d=0; d<dh[mi][i]; d++){
   dnewm=matrix(1,nlstate,1,npar);          newm=savm;
   doldm=matrix(1,nlstate,1,nlstate);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
            for (kk=1; kk<=cptcovage;kk++) {
   hstepm=1*YEARM; /* Every year of age */            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          }
   agelim = AGESUP;          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     if (stepm >= YEARM) hstepm=1;          /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
     gradg=matrix(1,npar,1,nlstate);          savm=oldm;
     gp=vector(1,nlstate);          oldm=newm;
     gm=vector(1,nlstate);        } /* end mult */
         
     for(theta=1; theta <=npar; theta++){        s1=s[mw[mi][i]][i];
       for(i=1; i<=npar; i++){ /* Computes gradient */        s2=s[mw[mi+1][i]][i];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        bbh=(double)bh[mi][i]/(double)stepm; 
       }        /* bias is positive if real duration
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);         * is higher than the multiple of stepm and negative otherwise.
       for(i=1;i<=nlstate;i++)         */
         gp[i] = prlim[i][i];        if( s2 > nlstate && (mle <5) ){  /* Jackson */
              lli=log(out[s1][s2] - savm[s1][s2]);
       for(i=1; i<=npar; i++) /* Computes gradient */        } else if  (s2==-2) {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          for (j=1,survp=0. ; j<=nlstate; j++) 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       for(i=1;i<=nlstate;i++)          lli= log(survp);
         gm[i] = prlim[i][i];        }else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       for(i=1;i<=nlstate;i++)        } else if(mle==2){
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          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 */
     } /* End theta */        } else if(mle==3){  /* exponential inter-extrapolation */
           lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     trgradg =matrix(1,nlstate,1,npar);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           lli=log(out[s1][s2]); /* Original formula */
     for(j=1; j<=nlstate;j++)        } else{  /* mle=0 back to 1 */
       for(theta=1; theta <=npar; theta++)          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         trgradg[j][theta]=gradg[theta][j];          /*lli=log(out[s1][s2]); */ /* Original formula */
         } /* End of if */
     for(i=1;i<=nlstate;i++)        ipmx +=1;
       varpl[i][(int)age] =0.;        sw += weight[i];
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     for(i=1;i<=nlstate;i++)        if(globpr){
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
    %11.6f %11.6f %11.6f ", \
     fprintf(ficresvpl,"%.0f ",age );                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     for(i=1; i<=nlstate;i++)                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
     fprintf(ficresvpl,"\n");            llt +=ll[k]*gipmx/gsw;
     free_vector(gp,1,nlstate);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     free_vector(gm,1,nlstate);          }
     free_matrix(gradg,1,npar,1,nlstate);          fprintf(ficresilk," %10.6f\n", -llt);
     free_matrix(trgradg,1,nlstate,1,npar);        }
   } /* End age */      } /* end of wave */
     } /* end of individual */
   free_vector(xp,1,npar);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   free_matrix(doldm,1,nlstate,1,npar);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   free_matrix(dnewm,1,nlstate,1,nlstate);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if(globpr==0){ /* First time we count the contributions and weights */
 }      gipmx=ipmx;
       gsw=sw;
 /************ Variance of one-step probabilities  ******************/    }
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    return -l;
 {  }
   int i, j, i1, k1, j1, z1;  
   int k=0,l, cptcode;  
   double **dnewm,**doldm;  /*************** function likelione ***********/
   double *xp;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   double *gp, *gm;  {
   double **gradg, **trgradg;    /* This routine should help understanding what is done with 
   double age,agelim, cov[NCOVMAX];       the selection of individuals/waves and
   int theta;       to check the exact contribution to the likelihood.
   char fileresprob[FILENAMELENGTH];       Plotting could be done.
   char fileresprobcov[FILENAMELENGTH];     */
   char fileresprobcor[FILENAMELENGTH];    int k;
   
   strcpy(fileresprob,"prob");    if(*globpri !=0){ /* Just counts and sums, no printings */
   strcat(fileresprob,fileres);      strcpy(fileresilk,"ilk"); 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      strcat(fileresilk,fileres);
     printf("Problem with resultfile: %s\n", fileresprob);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   }        printf("Problem with resultfile: %s\n", fileresilk);
   strcpy(fileresprobcov,"probcov");        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   strcat(fileresprobcov,fileres);      }
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {      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");
     printf("Problem with resultfile: %s\n", fileresprobcov);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   }      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   strcpy(fileresprobcor,"probcor");      for(k=1; k<=nlstate; k++) 
   strcat(fileresprobcor,fileres);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     printf("Problem with resultfile: %s\n", fileresprobcor);    }
   }  
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    *fretone=(*funcone)(p);
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    if(*globpri !=0){
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);      fclose(ficresilk);
        fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");      fflush(fichtm); 
   fprintf(ficresprob,"# Age");    } 
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    return;
   fprintf(ficresprobcov,"# Age");  }
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");  
   fprintf(ficresprobcov,"# Age");  
   for(i=1; i<=nlstate;i++)  /*********** Maximum Likelihood Estimation ***************/
     for(j=1; j<=(nlstate+ndeath);j++){  
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       fprintf(ficresprobcov," p%1d-%1d ",i,j);  {
       fprintf(ficresprobcor," p%1d-%1d ",i,j);    int i,j, iter;
     }      double **xi;
   fprintf(ficresprob,"\n");    double fret;
   fprintf(ficresprobcov,"\n");    double fretone; /* Only one call to likelihood */
   fprintf(ficresprobcor,"\n");    /*  char filerespow[FILENAMELENGTH];*/
   xp=vector(1,npar);    xi=matrix(1,npar,1,npar);
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    for (i=1;i<=npar;i++)
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      for (j=1;j<=npar;j++)
          xi[i][j]=(i==j ? 1.0 : 0.0);
   cov[1]=1;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   j=cptcoveff;    strcpy(filerespow,"pow"); 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    strcat(filerespow,fileres);
   j1=0;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   for(k1=1; k1<=1;k1++){      printf("Problem with resultfile: %s\n", filerespow);
     for(i1=1; i1<=ncodemax[k1];i1++){      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     j1++;    }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
     if  (cptcovn>0) {    for (i=1;i<=nlstate;i++)
       fprintf(ficresprob, "\n#********** Variable ");      for(j=1;j<=nlstate+ndeath;j++)
       fprintf(ficresprobcov, "\n#********** Variable ");        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       fprintf(ficresprobcor, "\n#********** Variable ");    fprintf(ficrespow,"\n");
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
       fprintf(ficresprob, "**********\n#");    powell(p,xi,npar,ftol,&iter,&fret,func);
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
       fprintf(ficresprobcov, "**********\n#");    free_matrix(xi,1,npar,1,npar);
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    fclose(ficrespow);
       fprintf(ficresprobcor, "**********\n#");    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     }    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
        fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       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]]];  /**** Computes Hessian and covariance matrix ***/
         }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  {
         for (k=1; k<=cptcovprod;k++)    double  **a,**y,*x,pd;
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    double **hess;
            int i, j,jk;
         gradg=matrix(1,npar,1,9);    int *indx;
         trgradg=matrix(1,9,1,npar);  
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
        void lubksb(double **a, int npar, int *indx, double b[]) ;
         for(theta=1; theta <=npar; theta++){    void ludcmp(double **a, int npar, int *indx, double *d) ;
           for(i=1; i<=npar; i++)    double gompertz(double p[]);
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    hess=matrix(1,npar,1,npar);
            
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    printf("\nCalculation of the hessian matrix. Wait...\n");
              fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
           k=0;    for (i=1;i<=npar;i++){
           for(i=1; i<= (nlstate+ndeath); i++){      printf("%d",i);fflush(stdout);
             for(j=1; j<=(nlstate+ndeath);j++){      fprintf(ficlog,"%d",i);fflush(ficlog);
               k=k+1;     
               gp[k]=pmmij[i][j];       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
             }      
           }      /*  printf(" %f ",p[i]);
                    printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
           for(i=1; i<=npar; i++)    }
             xp[i] = x[i] - (i==theta ?delti[theta]:0);    
        for (i=1;i<=npar;i++) {
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      for (j=1;j<=npar;j++)  {
           k=0;        if (j>i) { 
           for(i=1; i<=(nlstate+ndeath); i++){          printf(".%d%d",i,j);fflush(stdout);
             for(j=1; j<=(nlstate+ndeath);j++){          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
               k=k+1;          hess[i][j]=hessij(p,delti,i,j,func,npar);
               gm[k]=pmmij[i][j];          
             }          hess[j][i]=hess[i][j];    
           }          /*printf(" %lf ",hess[i][j]);*/
              }
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)      }
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      }
         }    printf("\n");
     fprintf(ficlog,"\n");
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)  
           for(theta=1; theta <=npar; theta++)    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
             trgradg[j][theta]=gradg[theta][j];    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
            
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    a=matrix(1,npar,1,npar);
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    y=matrix(1,npar,1,npar);
            x=vector(1,npar);
         pmij(pmmij,cov,ncovmodel,x,nlstate);    indx=ivector(1,npar);
            for (i=1;i<=npar;i++)
         k=0;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         for(i=1; i<=(nlstate+ndeath); i++){    ludcmp(a,npar,indx,&pd);
           for(j=1; j<=(nlstate+ndeath);j++){  
             k=k+1;    for (j=1;j<=npar;j++) {
             gm[k]=pmmij[i][j];      for (i=1;i<=npar;i++) x[i]=0;
           }      x[j]=1;
         }      lubksb(a,npar,indx,x);
            for (i=1;i<=npar;i++){ 
         /*printf("\n%d ",(int)age);        matcov[i][j]=x[i];
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    }
      }*/  
     printf("\n#Hessian matrix#\n");
         fprintf(ficresprob,"\n%d ",(int)age);    fprintf(ficlog,"\n#Hessian matrix#\n");
         fprintf(ficresprobcov,"\n%d ",(int)age);    for (i=1;i<=npar;i++) { 
         fprintf(ficresprobcor,"\n%d ",(int)age);      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)        fprintf(ficlog,"%.3e ",hess[i][j]);
           fprintf(ficresprob,"%12.3e (%12.3e) ",gm[i],sqrt(doldm[i][j]));      }
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){      printf("\n");
           fprintf(ficresprobcov,"%12.3e ",gm[i]);      fprintf(ficlog,"\n");
           fprintf(ficresprobcor,"%12.3e ",gm[i]);    }
         }  
         i=0;    /* Recompute Inverse */
         for (k=1; k<=(nlstate);k++){    for (i=1;i<=npar;i++)
           for (l=1; l<=(nlstate+ndeath);l++){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
             i=i++;    ludcmp(a,npar,indx,&pd);
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);  
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);    /*  printf("\n#Hessian matrix recomputed#\n");
             for (j=1; j<=i;j++){  
               fprintf(ficresprobcov," %12.3e",doldm[i][j]);    for (j=1;j<=npar;j++) {
               fprintf(ficresprobcor," %12.3e",doldm[i][j]/sqrt(doldm[i][i])/sqrt(doldm[j][j]));      for (i=1;i<=npar;i++) x[i]=0;
             }      x[j]=1;
           }      lubksb(a,npar,indx,x);
         }      for (i=1;i<=npar;i++){ 
       }        y[i][j]=x[i];
     }        printf("%.3e ",y[i][j]);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        fprintf(ficlog,"%.3e ",y[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);  
   fclose(ficresprobcov);    free_matrix(a,1,npar,1,npar);
   fclose(ficresprobcor);    free_matrix(y,1,npar,1,npar);
 }    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
 /******************* 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 optionfile[], \  
                   char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\  /*************** hessian matrix ****************/
                   char version[], int popforecast, int estepm ,\  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
                   double jprev1, double mprev1,double anprev1, \  {
                   double jprev2, double mprev2,double anprev2){    int i;
   int jj1, k1, i1, cpt;    int l=1, lmax=20;
   FILE *fichtm;    double k1,k2;
   /*char optionfilehtm[FILENAMELENGTH];*/    double p2[MAXPARM+1]; /* identical to x */
     double res;
   strcpy(optionfilehtm,optionfile);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   strcat(optionfilehtm,".htm");    double fx;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    int k=0,kmax=10;
     printf("Problem with %s \n",optionfilehtm), exit(0);    double l1;
   }  
     fx=func(x);
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    for (i=1;i<=npar;i++) p2[i]=x[i];
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    for(l=0 ; l <=lmax; l++){  /* Enlarging the zone around the Maximum */
 \n      l1=pow(10,l);
 Total number of observations=%d <br>\n      delts=delt;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n      for(k=1 ; k <kmax; k=k+1){
 <hr  size=\"2\" color=\"#EC5E5E\">        delt = delta*(l1*k);
  <ul><li>Parameter files<br>\n        p2[theta]=x[theta] +delt;
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n        k1=func(p2)-fx;   /* Might be negative if too close to the theoretical maximum */
  - 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);        p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n        /*res= (k1-2.0*fx+k2)/delt/delt; */
  - 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        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n        
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n  #ifdef DEBUGHESS
  - Life expectancies by age and initial health status (estepm=%2d months):        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);
    <a href=\"e%s\">e%s</a> <br>\n</li>", \        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);
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);  #endif
         /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n          k=kmax;
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n        }
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n          k=kmax; l=lmax*10.;
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n        }
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
  - 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);          delts=delt;
         }
  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    delti[theta]=delts;
         <br>",fileres,fileres,fileres,fileres);    return res; 
  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);  }
 fprintf(fichtm," <li>Graphs</li><p>");  
   double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
  m=cptcoveff;  {
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    int i;
     int l=1, l1, lmax=20;
  jj1=0;    double k1,k2,k3,k4,res,fx;
  for(k1=1; k1<=m;k1++){    double p2[MAXPARM+1];
    for(i1=1; i1<=ncodemax[k1];i1++){    int k;
      jj1++;  
      if (cptcovn > 0) {    fx=func(x);
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    for (k=1; k<=2; k++) {
        for (cpt=1; cpt<=cptcoveff;cpt++)      for (i=1;i<=npar;i++) p2[i]=x[i];
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);      p2[thetai]=x[thetai]+delti[thetai]/k;
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
      }      k1=func(p2)-fx;
      /* 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>      p2[thetai]=x[thetai]+delti[thetai]/k;
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          p2[thetaj]=x[thetaj]-delti[thetaj]/k;
      /* Quasi-incidences */      k2=func(p2)-fx;
      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);      p2[thetai]=x[thetai]-delti[thetai]/k;
        /* Stable prevalence in each health state */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
        for(cpt=1; cpt<nlstate;cpt++){      k3=func(p2)-fx;
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>    
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      p2[thetai]=x[thetai]-delti[thetai]/k;
        }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     for(cpt=1; cpt<=nlstate;cpt++) {      k4=func(p2)-fx;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
 interval) in state (%d): v%s%d%d.png <br>  #ifdef DEBUG
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
      }      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
      for(cpt=1; cpt<=nlstate;cpt++) {  #endif
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>    }
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    return res;
      }  }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  
 health expectancies in states (1) and (2): e%s%d.png<br>  /************** Inverse of matrix **************/
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  void ludcmp(double **a, int n, int *indx, double *d) 
 fprintf(fichtm,"\n</body>");  { 
    }    int i,imax,j,k; 
  }    double big,dum,sum,temp; 
 fclose(fichtm);    double *vv; 
 }   
     vv=vector(1,n); 
 /******************* Gnuplot file **************/    *d=1.0; 
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    for (i=1;i<=n;i++) { 
       big=0.0; 
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      for (j=1;j<=n;j++) 
   int ng;        if ((temp=fabs(a[i][j])) > big) big=temp; 
   strcpy(optionfilegnuplot,optionfilefiname);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   strcat(optionfilegnuplot,".gp");      vv[i]=1.0/big; 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    } 
     printf("Problem with file %s",optionfilegnuplot);    for (j=1;j<=n;j++) { 
   }      for (i=1;i<j;i++) { 
         sum=a[i][j]; 
 #ifdef windows        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     fprintf(ficgp,"cd \"%s\" \n",pathc);        a[i][j]=sum; 
 #endif      } 
 m=pow(2,cptcoveff);      big=0.0; 
        for (i=j;i<=n;i++) { 
  /* 1eme*/        sum=a[i][j]; 
   for (cpt=1; cpt<= nlstate ; cpt ++) {        for (k=1;k<j;k++) 
    for (k1=1; k1<= m ; k1 ++) {          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
 #ifdef windows        if ( (dum=vv[i]*fabs(sum)) >= big) { 
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          big=dum; 
      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);          imax=i; 
 #endif        } 
 #ifdef unix      } 
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      if (j != imax) { 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);        for (k=1;k<=n;k++) { 
 #endif          dum=a[imax][k]; 
           a[imax][k]=a[j][k]; 
 for (i=1; i<= nlstate ; i ++) {          a[j][k]=dum; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");        *d = -(*d); 
 }        vv[imax]=vv[j]; 
     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 ++) {      indx[j]=imax; 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      if (a[j][j] == 0.0) a[j][j]=TINY; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      if (j != n) { 
 }        dum=1.0/(a[j][j]); 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
      for (i=1; i<= nlstate ; i ++) {      } 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");    free_vector(vv,1,n);  /* Doesn't work */
 }    ;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%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");  void lubksb(double **a, int n, int *indx, double b[]) 
 #endif  { 
    }    int i,ii=0,ip,j; 
   }    double sum; 
   /*2 eme*/   
     for (i=1;i<=n;i++) { 
   for (k1=1; k1<= m ; k1 ++) {      ip=indx[i]; 
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);      sum=b[ip]; 
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);      b[ip]=b[i]; 
          if (ii) 
     for (i=1; i<= nlstate+1 ; i ++) {        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       k=2*i;      else if (sum) ii=i; 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      b[i]=sum; 
       for (j=1; j<= nlstate+1 ; j ++) {    } 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    for (i=n;i>=1;i--) { 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      sum=b[i]; 
 }        for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      b[i]=sum/a[i][i]; 
       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 ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  void pstamp(FILE *fichier)
         else fprintf(ficgp," \%%*lf (\%%*lf)");  {
 }      fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
       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 (j=1; j<= nlstate+1 ; j ++) {  /************ Frequencies ********************/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  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[])
   else fprintf(ficgp," \%%*lf (\%%*lf)");  {  /* Some frequencies */
 }      
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    int i, m, jk, k1,i1, j1, bool, z1,j;
       else fprintf(ficgp,"\" t\"\" w l 0,");    int first;
     }    double ***freq; /* Frequencies */
   }    double *pp, **prop;
      double pos,posprop, k2, dateintsum=0,k2cpt=0;
   /*3eme*/    char fileresp[FILENAMELENGTH];
     
   for (k1=1; k1<= m ; k1 ++) {    pp=vector(1,nlstate);
     for (cpt=1; cpt<= nlstate ; cpt ++) {    prop=matrix(1,nlstate,iagemin,iagemax+3);
       k=2+nlstate*(2*cpt-2);    strcpy(fileresp,"p");
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    strcat(fileresp,fileres);
       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);    if((ficresp=fopen(fileresp,"w"))==NULL) {
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      printf("Problem with prevalence resultfile: %s\n", fileresp);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      exit(0);
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    }
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    j1=0;
     
 */    j=cptcoveff;
       for (i=1; i< nlstate ; i ++) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         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);  
     first=1;
       }  
     }    /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */
   }    /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
      /*    j1++;
   /* CV preval stat */  */
     for (k1=1; k1<= m ; k1 ++) {    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
     for (cpt=1; cpt<nlstate ; cpt ++) {        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       k=3;          scanf("%d", i);*/
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        for (i=-5; i<=nlstate+ndeath; i++)  
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
             for(m=iagemin; m <= iagemax+3; m++)
       for (i=1; i< nlstate ; i ++)              freq[i][jk][m]=0;
         fprintf(ficgp,"+$%d",k+i+1);        
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        for (i=1; i<=nlstate; i++)  
                for(m=iagemin; m <= iagemax+3; m++)
       l=3+(nlstate+ndeath)*cpt;            prop[i][m]=0;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        
       for (i=1; i< nlstate ; i ++) {        dateintsum=0;
         l=3+(nlstate+ndeath)*cpt;        k2cpt=0;
         fprintf(ficgp,"+$%d",l+i+1);        for (i=1; i<=imx; i++) {
       }          bool=1;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
     }            for (z1=1; z1<=cptcoveff; z1++)       
   }                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
                    /* Tests if the value of each of the covariates of i is equal to filter j1 */
   /* proba elementaires */                bool=0;
    for(i=1,jk=1; i <=nlstate; i++){                /* 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", 
     for(k=1; k <=(nlstate+ndeath); k++){                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
       if (k != i) {                  j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
         for(j=1; j <=ncovmodel; j++){                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
                      } 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          }
           jk++;   
           fprintf(ficgp,"\n");          if (bool==1){
         }            for(m=firstpass; m<=lastpass; m++){
       }              k2=anint[m][i]+(mint[m][i]/12.);
     }              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
    }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
      for(jk=1; jk <=m; jk++) {                if (m<lastpass) {
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
        if (ng==2)                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");                }
        else                
          fprintf(ficgp,"\nset title \"Probability\"\n");                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);                  dateintsum=dateintsum+k2;
        i=1;                  k2cpt++;
        for(k2=1; k2<=nlstate; k2++) {                }
          k3=i;                /*}*/
          for(k=1; k<=(nlstate+ndeath); k++) {            }
            if (k != k2){          }
              if(ng==2)        } /* end i */
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);         
              else        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        pstamp(ficresp);
              ij=1;        if  (cptcovn>0) {
              for(j=3; j <=ncovmodel; j++) {          fprintf(ficresp, "\n#********** Variable "); 
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          fprintf(ficresp, "**********\n#");
                  ij++;          fprintf(ficlog, "\n#********** Variable "); 
                }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                else          fprintf(ficlog, "**********\n#");
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        }
              }        for(i=1; i<=nlstate;i++) 
              fprintf(ficgp,")/(1");          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
                      fprintf(ficresp, "\n");
              for(k1=1; k1 <=nlstate; k1++){          
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        for(i=iagemin; i <= iagemax+3; i++){
                ij=1;          if(i==iagemax+3){
                for(j=3; j <=ncovmodel; j++){            fprintf(ficlog,"Total");
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          }else{
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            if(first==1){
                    ij++;              first=0;
                  }              printf("See log file for details...\n");
                  else            }
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            fprintf(ficlog,"Age %d", i);
                }          }
                fprintf(ficgp,")");          for(jk=1; jk <=nlstate ; jk++){
              }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);              pp[jk] += freq[jk][m][i]; 
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          }
              i=i+ncovmodel;          for(jk=1; jk <=nlstate ; jk++){
            }            for(m=-1, pos=0; m <=0 ; m++)
          }              pos += freq[jk][m][i];
        }            if(pp[jk]>=1.e-10){
      }              if(first==1){
    }                printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
    fclose(ficgp);              }
 }  /* end gnuplot */              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
               if(first==1)
 /*************** Moving average **************/                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
   int i, cpt, cptcod;          }
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)  
       for (i=1; i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
           mobaverage[(int)agedeb][i][cptcod]=0.;              pp[jk] += freq[jk][m][i];
              }       
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       for (i=1; i<=nlstate;i++){            pos += pp[jk];
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){            posprop += prop[jk][i];
           for (cpt=0;cpt<=4;cpt++){          }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          for(jk=1; jk <=nlstate ; jk++){
           }            if(pos>=1.e-5){
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;              if(first==1)
         }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       }              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     }            }else{
                  if(first==1)
 }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
 /************** Forecasting ******************/            if( i <= iagemax){
 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){              if(pos>=1.e-5){
                  fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                /*probs[i][jk][j1]= pp[jk]/pos;*/
   int *popage;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;              }
   double *popeffectif,*popcount;              else
   double ***p3mat;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   char fileresf[FILENAMELENGTH];            }
           }
  agelim=AGESUP;          
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          for(jk=-1; jk <=nlstate+ndeath; jk++)
             for(m=-1; m <=nlstate+ndeath; m++)
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);              if(freq[jk][m][i] !=0 ) {
                if(first==1)
                  printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   strcpy(fileresf,"f");                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   strcat(fileresf,fileres);              }
   if((ficresf=fopen(fileresf,"w"))==NULL) {          if(i <= iagemax)
     printf("Problem with forecast resultfile: %s\n", fileresf);            fprintf(ficresp,"\n");
   }          if(first==1)
   printf("Computing forecasting: result on file '%s' \n", fileresf);            printf("Others in log...\n");
           fprintf(ficlog,"\n");
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        }
         /*}*/
   if (mobilav==1) {    }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    dateintmean=dateintsum/k2cpt; 
     movingaverage(agedeb, fage, ageminpar, mobaverage);   
   }    fclose(ficresp);
     free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    free_vector(pp,1,nlstate);
   if (stepm<=12) stepsize=1;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
      /* End of Freq */
   agelim=AGESUP;  }
    
   hstepm=1;  /************ Prevalence ********************/
   hstepm=hstepm/stepm;  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)
   yp1=modf(dateintmean,&yp);  {  
   anprojmean=yp;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   yp2=modf((yp1*12),&yp);       in each health status at the date of interview (if between dateprev1 and dateprev2).
   mprojmean=yp;       We still use firstpass and lastpass as another selection.
   yp1=modf((yp2*30.5),&yp);    */
   jprojmean=yp;   
   if(jprojmean==0) jprojmean=1;    int i, m, jk, k1, i1, j1, bool, z1,j;
   if(mprojmean==0) jprojmean=1;    double ***freq; /* Frequencies */
      double *pp, **prop;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    double pos,posprop; 
      double  y2; /* in fractional years */
   for(cptcov=1;cptcov<=i2;cptcov++){    int iagemin, iagemax;
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    int first; /** to stop verbosity which is redirected to log file */
       k=k+1;  
       fprintf(ficresf,"\n#******");    iagemin= (int) agemin;
       for(j=1;j<=cptcoveff;j++) {    iagemax= (int) agemax;
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /*pp=vector(1,nlstate);*/
       }    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       fprintf(ficresf,"******\n");    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       fprintf(ficresf,"# StartingAge FinalAge");    j1=0;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    
          /*j=cptcoveff;*/
          if (cptcovn<1) {j=1;ncodemax[1]=1;}
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    
         fprintf(ficresf,"\n");    first=1;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
       /*for(i1=1; i1<=ncodemax[k1];i1++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        j1++;*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        
           nhstepm = nhstepm/hstepm;        for (i=1; i<=nlstate; i++)  
                    for(m=iagemin; m <= iagemax+3; m++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            prop[i][m]=0.0;
           oldm=oldms;savm=savms;       
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for (i=1; i<=imx; i++) { /* Each individual */
                  bool=1;
           for (h=0; h<=nhstepm; h++){          if  (cptcovn>0) {
             if (h==(int) (calagedate+YEARM*cpt)) {            for (z1=1; z1<=cptcoveff; z1++) 
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
             }                bool=0;
             for(j=1; j<=nlstate+ndeath;j++) {          } 
               kk1=0.;kk2=0;          if (bool==1) { 
               for(i=1; i<=nlstate;i++) {                          for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
                 if (mobilav==1)              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                 else {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                                if (s[m][i]>0 && s[m][i]<=nlstate) { 
               }                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
               if (h==(int)(calagedate+12*cpt)){                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                 fprintf(ficresf," %.3f", kk1);                  prop[s[m][i]][iagemax+3] += weight[i]; 
                                        } 
               }              }
             }            } /* end selection of waves */
           }          }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
         }        for(i=iagemin; i <= iagemax+3; i++){  
       }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     }            posprop += prop[jk][i]; 
   }          } 
                  
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(jk=1; jk <=nlstate ; jk++){     
             if( i <=  iagemax){ 
   fclose(ficresf);              if(posprop>=1.e-5){ 
 }                probs[i][jk][j1]= prop[jk][i]/posprop;
 /************** Forecasting ******************/              } else{
 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(first==1){
                    first=0;
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                  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]);
   int *popage;                }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;              }
   double *popeffectif,*popcount;            } 
   double ***p3mat,***tabpop,***tabpopprev;          }/* end jk */ 
   char filerespop[FILENAMELENGTH];        }/* end i */ 
       /*} *//* end i1 */
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    } /* end j1 */
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    
   agelim=AGESUP;    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    /*free_vector(pp,1,nlstate);*/
      free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  }  /* End of prevalence */
    
    /************* Waves Concatenation ***************/
   strcpy(filerespop,"pop");  
   strcat(filerespop,fileres);  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((ficrespop=fopen(filerespop,"w"))==NULL) {  {
     printf("Problem with forecast resultfile: %s\n", filerespop);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   }       Death is a valid wave (if date is known).
   printf("Computing forecasting: result on file '%s' \n", filerespop);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
        dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   if (cptcoveff==0) ncodemax[cptcoveff]=1;       and mw[mi+1][i]. dh depends on stepm.
        */
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int i, mi, m;
     movingaverage(agedeb, fage, ageminpar, mobaverage);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   }       double sum=0., jmean=0.;*/
     int first;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    int j, k=0,jk, ju, jl;
   if (stepm<=12) stepsize=1;    double sum=0.;
      first=0;
   agelim=AGESUP;    jmin=1e+5;
      jmax=-1;
   hstepm=1;    jmean=0.;
   hstepm=hstepm/stepm;    for(i=1; i<=imx; i++){
        mi=0;
   if (popforecast==1) {      m=firstpass;
     if((ficpop=fopen(popfile,"r"))==NULL) {      while(s[m][i] <= nlstate){
       printf("Problem with population file : %s\n",popfile);exit(0);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
     }          mw[++mi][i]=m;
     popage=ivector(0,AGESUP);        if(m >=lastpass)
     popeffectif=vector(0,AGESUP);          break;
     popcount=vector(0,AGESUP);        else
              m++;
     i=1;        }/* end while */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;      if (s[m][i] > nlstate){
            mi++;     /* Death is another wave */
     imx=i;        /* if(mi==0)  never been interviewed correctly before death */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];           /* Only death is a correct wave */
   }        mw[mi][i]=m;
       }
   for(cptcov=1;cptcov<=i2;cptcov++){  
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      wav[i]=mi;
       k=k+1;      if(mi==0){
       fprintf(ficrespop,"\n#******");        nbwarn++;
       for(j=1;j<=cptcoveff;j++) {        if(first==0){
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       }          first=1;
       fprintf(ficrespop,"******\n");        }
       fprintf(ficrespop,"# Age");        if(first==1){
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
       if (popforecast==1)  fprintf(ficrespop," [Population]");        }
            } /* end mi==0 */
       for (cpt=0; cpt<=0;cpt++) {    } /* End individuals */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    
            for(i=1; i<=imx; i++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      for(mi=1; mi<wav[i];mi++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        if (stepm <=0)
           nhstepm = nhstepm/hstepm;          dh[mi][i]=1;
                  else{
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           oldm=oldms;savm=savms;            if (agedc[i] < 2*AGESUP) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                      if(j==0) j=1;  /* Survives at least one month after exam */
           for (h=0; h<=nhstepm; h++){              else if(j<0){
             if (h==(int) (calagedate+YEARM*cpt)) {                nberr++;
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             }                j=1; /* Temporary Dangerous patch */
             for(j=1; j<=nlstate+ndeath;j++) {                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               kk1=0.;kk2=0;                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               for(i=1; i<=nlstate;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 (mobilav==1)              }
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];              k=k+1;
                 else {              if (j >= jmax){
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                jmax=j;
                 }                ijmax=i;
               }              }
               if (h==(int)(calagedate+12*cpt)){              if (j <= jmin){
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;                jmin=j;
                   /*fprintf(ficrespop," %.3f", kk1);                ijmin=i;
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/              }
               }              sum=sum+j;
             }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
             for(i=1; i<=nlstate;i++){              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
               kk1=0.;            }
                 for(j=1; j<=nlstate;j++){          }
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          else{
                 }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
             }  
             k=k+1;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)            if (j >= jmax) {
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);              jmax=j;
           }              ijmax=i;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
         }            else if (j <= jmin){
       }              jmin=j;
                ijmin=i;
   /******/            }
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);              if(j<0){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              nberr++;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              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]);
           nhstepm = nhstepm/hstepm;              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]);
                      }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            sum=sum+j;
           oldm=oldms;savm=savms;          }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            jk= j/stepm;
           for (h=0; h<=nhstepm; h++){          jl= j -jk*stepm;
             if (h==(int) (calagedate+YEARM*cpt)) {          ju= j -(jk+1)*stepm;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             }            if(jl==0){
             for(j=1; j<=nlstate+ndeath;j++) {              dh[mi][i]=jk;
               kk1=0.;kk2=0;              bh[mi][i]=0;
               for(i=1; i<=nlstate;i++) {                          }else{ /* We want a negative bias in order to only have interpolation ie
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                        * to avoid the price of an extra matrix product in likelihood */
               }              dh[mi][i]=jk+1;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);              bh[mi][i]=ju;
             }            }
           }          }else{
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            if(jl <= -ju){
         }              dh[mi][i]=jk;
       }              bh[mi][i]=jl;       /* bias is positive if real duration
    }                                   * is higher than the multiple of stepm and negative otherwise.
   }                                   */
              }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            else{
               dh[mi][i]=jk+1;
   if (popforecast==1) {              bh[mi][i]=ju;
     free_ivector(popage,0,AGESUP);            }
     free_vector(popeffectif,0,AGESUP);            if(dh[mi][i]==0){
     free_vector(popcount,0,AGESUP);              dh[mi][i]=1; /* At least one step */
   }              bh[mi][i]=ju; /* At least one step */
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              /*  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);*/
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            }
   fclose(ficrespop);          } /* end if mle */
 }        }
       } /* end wave */
 /***********************************************/    }
 /**************** Main Program *****************/    jmean=sum/k;
 /***********************************************/    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);
 int main(int argc, char *argv[])   }
 {  
   /*********** Tricode ****************************/
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
   double agedeb, agefin,hf;  {
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
     /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
   double fret;    /* Boring subroutine which should only output nbcode[Tvar[j]][k]
   double **xi,tmp,delta;     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
     /* nbcode[Tvar[j]][1]= 
   double dum; /* Dummy variable */    */
   double ***p3mat;  
   int *indx;    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   char line[MAXLINE], linepar[MAXLINE];    int modmaxcovj=0; /* Modality max of covariates j */
   char title[MAXLINE];    int cptcode=0; /* Modality max of covariates j */
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    int modmincovj=0; /* Modality min of covariates j */
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  
    
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    cptcoveff=0; 
    
   char filerest[FILENAMELENGTH];    for (k=-1; k < maxncov; k++) Ndum[k]=0;
   char fileregp[FILENAMELENGTH];    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   char popfile[FILENAMELENGTH];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    /* Loop on covariates without age and products */
   int firstobs=1, lastobs=10;    for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
   int sdeb, sfin; /* Status at beginning and end */      for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the 
   int c,  h , cpt,l;                                 modality of this covariate Vj*/ 
   int ju,jl, mi;        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;                                      * If product of Vn*Vm, still boolean *:
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;                                      * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
   int mobilav=0,popforecast=0;                                      * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
   int hstepm, nhstepm;        /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;                                        modality of the nth covariate of individual i. */
         if (ij > modmaxcovj)
   double bage, fage, age, agelim, agebase;          modmaxcovj=ij; 
   double ftolpl=FTOL;        else if (ij < modmincovj) 
   double **prlim;          modmincovj=ij; 
   double *severity;        if ((ij < -1) && (ij > NCOVMAX)){
   double ***param; /* Matrix of parameters */          printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
   double  *p;          exit(1);
   double **matcov; /* Matrix of covariance */        }else
   double ***delti3; /* Scale */        Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
   double *delti; /* Scale */        /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
   double ***eij, ***vareij;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   double **varpl; /* Variances of prevalence limits by age */        /* getting the maximum value of the modality of the covariate
   double *epj, vepp;           (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
   double kk1, kk2;           female is 1, then modmaxcovj=1.*/
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;      }
        printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
       cptcode=modmaxcovj;
   char version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";      /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
   char *alph[]={"a","a","b","c","d","e"}, str[4];     /*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 */
         printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
   char z[1]="c", occ;        if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
 #include <sys/time.h>          ncodemax[j]++;  /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
 #include <time.h>        }
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for
             historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
   /* long total_usecs;      } /* Ndum[-1] number of undefined modalities */
   struct timeval start_time, end_time;  
        /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
   getcwd(pathcd, size);      /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
          modmincovj=3; modmaxcovj = 7;
   printf("\n%s",version);         There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
   if(argc <=1){         which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy 
     printf("\nEnter the parameter file name: ");         variables V1_1 and V1_2.
     scanf("%s",pathtot);         nbcode[Tvar[j]][ij]=k;
   }         nbcode[Tvar[j]][1]=0;
   else{         nbcode[Tvar[j]][2]=1;
     strcpy(pathtot,argv[1]);         nbcode[Tvar[j]][3]=2;
   }      */
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/      ij=1; /* ij is similar to i but can jumps over null modalities */
   /*cygwin_split_path(pathtot,path,optionfile);      for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
   /* cutv(path,optionfile,pathtot,'\\');*/          /*recode from 0 */
           if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);            nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode. 
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);                                       k is a modality. If we have model=V1+V1*sex 
   chdir(path);                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
   replace(pathc,path);            ij++;
           }
 /*-------- arguments in the command line --------*/          if (ij > ncodemax[j]) break; 
         }  /* end of loop on */
   strcpy(fileres,"r");      } /* end of loop on modality */ 
   strcat(fileres, optionfilefiname);    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/  
   strcat(fileres,".txt");    /* Other files have txt extension */    
    for (k=-1; k< maxncov; k++) Ndum[k]=0; 
   /*---------arguments file --------*/    
     for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */ 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
     printf("Problem with optionfile %s\n",optionfile);     ij=Tvar[i]; /* Tvar might be -1 if status was unknown */ 
     goto end;     Ndum[ij]++; 
   }   } 
   
   strcpy(filereso,"o");   ij=1;
   strcat(filereso,fileres);   for (i=0; i<=  maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
   if((ficparo=fopen(filereso,"w"))==NULL) {     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
     printf("Problem with Output resultfile: %s\n", filereso);goto end;     if((Ndum[i]!=0) && (i<=ncovcol)){
   }       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
        Tvaraff[ij]=i; /*For printing (unclear) */
   /* Reads comments: lines beginning with '#' */       ij++;
   while((c=getc(ficpar))=='#' && c!= EOF){     }else
     ungetc(c,ficpar);         Tvaraff[ij]=0;
     fgets(line, MAXLINE, ficpar);   }
     puts(line);   ij--;
     fputs(line,ficparo);   cptcoveff=ij; /*Number of total covariates*/
   }  
   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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);  
   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);  /*********** Health Expectancies ****************/
   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);  
 while((c=getc(ficpar))=='#' && c!= EOF){  void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  {
     puts(line);    /* Health expectancies, no variances */
     fputs(line,ficparo);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   }    int nhstepma, nstepma; /* Decreasing with age */
   ungetc(c,ficpar);    double age, agelim, hf;
      double ***p3mat;
        double eip;
   covar=matrix(0,NCOVMAX,1,n);  
   cptcovn=0;    pstamp(ficreseij);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     fprintf(ficreseij,"# Age");
   ncovmodel=2+cptcovn;    for(i=1; i<=nlstate;i++){
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      for(j=1; j<=nlstate;j++){
          fprintf(ficreseij," e%1d%1d ",i,j);
   /* Read guess parameters */      }
   /* Reads comments: lines beginning with '#' */      fprintf(ficreseij," e%1d. ",i);
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    fprintf(ficreseij,"\n");
     fgets(line, MAXLINE, ficpar);  
     puts(line);    
     fputs(line,ficparo);    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
   ungetc(c,ficpar);    }
      else  hstepm=estepm;   
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    /* We compute the life expectancy from trapezoids spaced every estepm months
     for(i=1; i <=nlstate; i++)     * This is mainly to measure the difference between two models: for example
     for(j=1; j <=nlstate+ndeath-1; j++){     * if stepm=24 months pijx are given only every 2 years and by summing them
       fscanf(ficpar,"%1d%1d",&i1,&j1);     * we are calculating an estimate of the Life Expectancy assuming a linear 
       fprintf(ficparo,"%1d%1d",i1,j1);     * progression in between and thus overestimating or underestimating according
       printf("%1d%1d",i,j);     * to the curvature of the survival function. If, for the same date, we 
       for(k=1; k<=ncovmodel;k++){     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         fscanf(ficpar," %lf",&param[i][j][k]);     * to compare the new estimate of Life expectancy with the same linear 
         printf(" %lf",param[i][j][k]);     * hypothesis. A more precise result, taking into account a more precise
         fprintf(ficparo," %lf",param[i][j][k]);     * curvature will be obtained if estepm is as small as stepm. */
       }  
       fscanf(ficpar,"\n");    /* For example we decided to compute the life expectancy with the smallest unit */
       printf("\n");    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       fprintf(ficparo,"\n");       nhstepm is the number of hstepm from age to agelim 
     }       nstepm is the number of stepm from age to agelin. 
         Look at hpijx to understand the reason of that which relies in memory size
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   p=param[1][1];       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
   /* Reads comments: lines beginning with '#' */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   while((c=getc(ficpar))=='#' && c!= EOF){       results. So we changed our mind and took the option of the best precision.
     ungetc(c,ficpar);    */
     fgets(line, MAXLINE, ficpar);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     puts(line);  
     fputs(line,ficparo);    agelim=AGESUP;
   }    /* If stepm=6 months */
   ungetc(c,ficpar);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  /* nhstepm age range expressed in number of stepm */
   for(i=1; i <=nlstate; i++){    nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
     for(j=1; j <=nlstate+ndeath-1; j++){    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       fscanf(ficpar,"%1d%1d",&i1,&j1);    /* if (stepm >= YEARM) hstepm=1;*/
       printf("%1d%1d",i,j);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       fprintf(ficparo,"%1d%1d",i1,j1);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar,"%le",&delti3[i][j][k]);    for (age=bage; age<=fage; age ++){ 
         printf(" %le",delti3[i][j][k]);      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
         fprintf(ficparo," %le",delti3[i][j][k]);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       }      /* if (stepm >= YEARM) hstepm=1;*/
       fscanf(ficpar,"\n");      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
       printf("\n");  
       fprintf(ficparo,"\n");      /* If stepm=6 months */
     }      /* Computed by stepm unit matrices, product of hstepma matrices, stored
   }         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
   delti=delti3[1][1];      
        hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   /* Reads comments: lines beginning with '#' */      
   while((c=getc(ficpar))=='#' && c!= EOF){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     ungetc(c,ficpar);      
     fgets(line, MAXLINE, ficpar);      printf("%d|",(int)age);fflush(stdout);
     puts(line);      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     fputs(line,ficparo);      
   }      /* Computing expectancies */
   ungetc(c,ficpar);      for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++)
   matcov=matrix(1,npar,1,npar);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   for(i=1; i <=npar; i++){            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     fscanf(ficpar,"%s",&str);            
     printf("%s",str);            /* 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]);*/
     fprintf(ficparo,"%s",str);  
     for(j=1; j <=i; j++){          }
       fscanf(ficpar," %le",&matcov[i][j]);  
       printf(" %.5le",matcov[i][j]);      fprintf(ficreseij,"%3.0f",age );
       fprintf(ficparo," %.5le",matcov[i][j]);      for(i=1; i<=nlstate;i++){
     }        eip=0;
     fscanf(ficpar,"\n");        for(j=1; j<=nlstate;j++){
     printf("\n");          eip +=eij[i][j][(int)age];
     fprintf(ficparo,"\n");          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   }        }
   for(i=1; i <=npar; i++)        fprintf(ficreseij,"%9.4f", eip );
     for(j=i+1;j<=npar;j++)      }
       matcov[i][j]=matcov[j][i];      fprintf(ficreseij,"\n");
          
   printf("\n");    }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     /*-------- Rewriting paramater file ----------*/    fprintf(ficlog,"\n");
      strcpy(rfileres,"r");    /* "Rparameterfile */    
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/  }
      strcat(rfileres,".");    /* */  
      strcat(rfileres,optionfilext);    /* Other files have txt extension */  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[] )
     if((ficres =fopen(rfileres,"w"))==NULL) {  
       printf("Problem writing new parameter file: %s\n", fileres);goto end;  {
     }    /* Covariances of health expectancies eij and of total life expectancies according
     fprintf(ficres,"#%s\n",version);     to initial status i, ei. .
        */
     /*-------- data file ----------*/    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
     if((fic=fopen(datafile,"r"))==NULL)    {    int nhstepma, nstepma; /* Decreasing with age */
       printf("Problem with datafile: %s\n", datafile);goto end;    double age, agelim, hf;
     }    double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
     n= lastobs;    double *xp, *xm;
     severity = vector(1,maxwav);    double **gp, **gm;
     outcome=imatrix(1,maxwav+1,1,n);    double ***gradg, ***trgradg;
     num=ivector(1,n);    int theta;
     moisnais=vector(1,n);  
     annais=vector(1,n);    double eip, vip;
     moisdc=vector(1,n);  
     andc=vector(1,n);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     agedc=vector(1,n);    xp=vector(1,npar);
     cod=ivector(1,n);    xm=vector(1,npar);
     weight=vector(1,n);    dnewm=matrix(1,nlstate*nlstate,1,npar);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     mint=matrix(1,maxwav,1,n);    
     anint=matrix(1,maxwav,1,n);    pstamp(ficresstdeij);
     s=imatrix(1,maxwav+1,1,n);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
     adl=imatrix(1,maxwav+1,1,n);        fprintf(ficresstdeij,"# Age");
     tab=ivector(1,NCOVMAX);    for(i=1; i<=nlstate;i++){
     ncodemax=ivector(1,8);      for(j=1; j<=nlstate;j++)
         fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
     i=1;      fprintf(ficresstdeij," e%1d. ",i);
     while (fgets(line, MAXLINE, fic) != NULL)    {    }
       if ((i >= firstobs) && (i <=lastobs)) {    fprintf(ficresstdeij,"\n");
          
         for (j=maxwav;j>=1;j--){    pstamp(ficrescveij);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
           strcpy(line,stra);    fprintf(ficrescveij,"# Age");
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    for(i=1; i<=nlstate;i++)
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      for(j=1; j<=nlstate;j++){
         }        cptj= (j-1)*nlstate+i;
                for(i2=1; i2<=nlstate;i2++)
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);          for(j2=1; j2<=nlstate;j2++){
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);            cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          }
       }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficrescveij,"\n");
         for (j=ncovcol;j>=1;j--){    
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    if(estepm < stepm){
         }      printf ("Problem %d lower than %d\n",estepm, stepm);
         num[i]=atol(stra);    }
            else  hstepm=estepm;   
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    /* We compute the life expectancy from trapezoids spaced every estepm months
           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;}*/     * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
         i=i+1;     * we are calculating an estimate of the Life Expectancy assuming a linear 
       }     * progression in between and thus overestimating or underestimating according
     }     * to the curvature of the survival function. If, for the same date, we 
     /* printf("ii=%d", ij);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
        scanf("%d",i);*/     * to compare the new estimate of Life expectancy with the same linear 
   imx=i-1; /* Number of individuals */     * hypothesis. A more precise result, taking into account a more precise
      * curvature will be obtained if estepm is as small as stepm. */
   /* for (i=1; i<=imx; i++){  
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    /* For example we decided to compute the life expectancy with the smallest unit */
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;       nhstepm is the number of hstepm from age to agelim 
     }*/       nstepm is the number of stepm from age to agelin. 
    /*  for (i=1; i<=imx; i++){       Look at hpijx to understand the reason of that which relies in memory size
      if (s[4][i]==9)  s[4][i]=-1;       and note for a fixed period like estepm months */
      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]));}*/    /* 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
   /* Calculation of the number of parameter from char model*/       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   Tvar=ivector(1,15);       results. So we changed our mind and took the option of the best precision.
   Tprod=ivector(1,15);    */
   Tvaraff=ivector(1,15);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);          /* If stepm=6 months */
        /* nhstepm age range expressed in number of stepm */
   if (strlen(model) >1){    agelim=AGESUP;
     j=0, j1=0, k1=1, k2=1;    nstepm=(int) rint((agelim-bage)*YEARM/stepm); 
     j=nbocc(model,'+');    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     j1=nbocc(model,'*');    /* if (stepm >= YEARM) hstepm=1;*/
     cptcovn=j+1;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     cptcovprod=j1;    
        p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     strcpy(modelsav,model);    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       printf("Error. Non available option model=%s ",model);    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
       goto end;    gp=matrix(0,nhstepm,1,nlstate*nlstate);
     }    gm=matrix(0,nhstepm,1,nlstate*nlstate);
      
     for(i=(j+1); i>=1;i--){    for (age=bage; age<=fage; age ++){ 
       cutv(stra,strb,modelsav,'+');      nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      /* if (stepm >= YEARM) hstepm=1;*/
       /*scanf("%d",i);*/      nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
       if (strchr(strb,'*')) {  
         cutv(strd,strc,strb,'*');      /* If stepm=6 months */
         if (strcmp(strc,"age")==0) {      /* Computed by stepm unit matrices, product of hstepma matrices, stored
           cptcovprod--;         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           cutv(strb,stre,strd,'V');      
           Tvar[i]=atoi(stre);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           cptcovage++;  
             Tage[cptcovage]=i;      /* Computing  Variances of health expectancies */
             /*printf("stre=%s ", stre);*/      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
         }         decrease memory allocation */
         else if (strcmp(strd,"age")==0) {      for(theta=1; theta <=npar; theta++){
           cptcovprod--;        for(i=1; i<=npar; i++){ 
           cutv(strb,stre,strc,'V');          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           Tvar[i]=atoi(stre);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
           cptcovage++;        }
           Tage[cptcovage]=i;        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         }        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
         else {    
           cutv(strb,stre,strc,'V');        for(j=1; j<= nlstate; j++){
           Tvar[i]=ncovcol+k1;          for(i=1; i<=nlstate; i++){
           cutv(strb,strc,strd,'V');            for(h=0; h<=nhstepm-1; h++){
           Tprod[k1]=i;              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
           Tvard[k1][1]=atoi(strc);              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
           Tvard[k1][2]=atoi(stre);            }
           Tvar[cptcovn+k2]=Tvard[k1][1];          }
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        }
           for (k=1; k<=lastobs;k++)       
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];        for(ij=1; ij<= nlstate*nlstate; ij++)
           k1++;          for(h=0; h<=nhstepm-1; h++){
           k2=k2+2;            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
         }          }
       }      }/* End theta */
       else {      
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      
        /*  scanf("%d",i);*/      for(h=0; h<=nhstepm-1; h++)
       cutv(strd,strc,strb,'V');        for(j=1; j<=nlstate*nlstate;j++)
       Tvar[i]=atoi(strc);          for(theta=1; theta <=npar; theta++)
       }            trgradg[h][j][theta]=gradg[h][theta][j];
       strcpy(modelsav,stra);        
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  
         scanf("%d",i);*/       for(ij=1;ij<=nlstate*nlstate;ij++)
     }        for(ji=1;ji<=nlstate*nlstate;ji++)
 }          varhe[ij][ji][(int)age] =0.;
    
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);       printf("%d|",(int)age);fflush(stdout);
   printf("cptcovprod=%d ", cptcovprod);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   scanf("%d ",i);*/       for(h=0;h<=nhstepm-1;h++){
     fclose(fic);        for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     /*  if(mle==1){*/          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     if (weightopt != 1) { /* Maximisation without weights*/          for(ij=1;ij<=nlstate*nlstate;ij++)
       for(i=1;i<=n;i++) weight[i]=1.0;            for(ji=1;ji<=nlstate*nlstate;ji++)
     }              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     /*-calculation of age at interview from date of interview and age at death -*/        }
     agev=matrix(1,maxwav,1,imx);      }
   
     for (i=1; i<=imx; i++) {      /* Computing expectancies */
       for(m=2; (m<= maxwav); m++) {      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      for(i=1; i<=nlstate;i++)
          anint[m][i]=9999;        for(j=1; j<=nlstate;j++)
          s[m][i]=-1;          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;
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;            
       }            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     }  
           }
     for (i=1; i<=imx; i++)  {  
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      fprintf(ficresstdeij,"%3.0f",age );
       for(m=1; (m<= maxwav); m++){      for(i=1; i<=nlstate;i++){
         if(s[m][i] >0){        eip=0.;
           if (s[m][i] >= nlstate+1) {        vip=0.;
             if(agedc[i]>0)        for(j=1; j<=nlstate;j++){
               if(moisdc[i]!=99 && andc[i]!=9999)          eip += eij[i][j][(int)age];
                 agev[m][i]=agedc[i];          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
            else {          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
               if (andc[i]!=9999){        }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
               agev[m][i]=-1;      }
               }      fprintf(ficresstdeij,"\n");
             }  
           }      fprintf(ficrescveij,"%3.0f",age );
           else if(s[m][i] !=9){ /* Should no more exist */      for(i=1; i<=nlstate;i++)
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        for(j=1; j<=nlstate;j++){
             if(mint[m][i]==99 || anint[m][i]==9999)          cptj= (j-1)*nlstate+i;
               agev[m][i]=1;          for(i2=1; i2<=nlstate;i2++)
             else if(agev[m][i] <agemin){            for(j2=1; j2<=nlstate;j2++){
               agemin=agev[m][i];              cptj2= (j2-1)*nlstate+i2;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/              if(cptj2 <= cptj)
             }                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             else if(agev[m][i] >agemax){            }
               agemax=agev[m][i];        }
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      fprintf(ficrescveij,"\n");
             }     
             /*agev[m][i]=anint[m][i]-annais[i];*/    }
             /*   agev[m][i] = age[i]+2*m;*/    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           }    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
           else { /* =9 */    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
             agev[m][i]=1;    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
             s[m][i]=-1;    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }    printf("\n");
         else /*= 0 Unknown */    fprintf(ficlog,"\n");
           agev[m][i]=1;  
       }    free_vector(xm,1,npar);
        free_vector(xp,1,npar);
     }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     for (i=1; i<=imx; i++)  {    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       for(m=1; (m<= maxwav); m++){    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
         if (s[m][i] > (nlstate+ndeath)) {  }
           printf("Error: Wrong value in nlstate or ndeath\n");    
           goto end;  /************ Variance ******************/
         }  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[])
       }  {
     }    /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    /* double **newm;*/
     double **dnewm,**doldm;
     free_vector(severity,1,maxwav);    double **dnewmp,**doldmp;
     free_imatrix(outcome,1,maxwav+1,1,n);    int i, j, nhstepm, hstepm, h, nstepm ;
     free_vector(moisnais,1,n);    int k, cptcode;
     free_vector(annais,1,n);    double *xp;
     /* free_matrix(mint,1,maxwav,1,n);    double **gp, **gm;  /* for var eij */
        free_matrix(anint,1,maxwav,1,n);*/    double ***gradg, ***trgradg; /*for var eij */
     free_vector(moisdc,1,n);    double **gradgp, **trgradgp; /* for var p point j */
     free_vector(andc,1,n);    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
        double ***p3mat;
     wav=ivector(1,imx);    double age,agelim, hf;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    double ***mobaverage;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    int theta;
        char digit[4];
     /* Concatenates waves */    char digitp[25];
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
     char fileresprobmorprev[FILENAMELENGTH];
   
       Tcode=ivector(1,100);    if(popbased==1){
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      if(mobilav!=0)
       ncodemax[1]=1;        strcpy(digitp,"-populbased-mobilav-");
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      else strcpy(digitp,"-populbased-nomobil-");
          }
    codtab=imatrix(1,100,1,10);    else 
    h=0;      strcpy(digitp,"-stablbased-");
    m=pow(2,cptcoveff);  
      if (mobilav!=0) {
    for(k=1;k<=cptcoveff; k++){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      for(i=1; i <=(m/pow(2,k));i++){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
        for(j=1; j <= ncodemax[k]; j++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        printf(" Error in movingaverage mobilav=%d\n",mobilav);
            h++;      }
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;    }
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/  
          }    strcpy(fileresprobmorprev,"prmorprev"); 
        }    sprintf(digit,"%-d",ij);
      }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
    }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
       codtab[1][2]=1;codtab[2][2]=2; */    strcat(fileresprobmorprev,fileres);
    /* for(i=1; i <=m ;i++){    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       for(k=1; k <=cptcovn; k++){      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       }    }
       printf("\n");    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       }   
       scanf("%d",i);*/    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
        pstamp(ficresprobmorprev);
    /* Calculates basic frequencies. Computes observed prevalence at single age    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);
        and prints on file fileres'p'. */    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprobmorprev," p.%-d SE",j);
          for(i=1; i<=nlstate;i++)
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }  
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprobmorprev,"\n");
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficgp,"\n# Routine varevsij");
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
          fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     /* For Powell, parameters are in a vector p[] starting at p[1]    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
        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) */    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     if(mle==1){    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    if(popbased==1)
     }      fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
        else
     /*--------- results files --------------*/      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     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(ficresvij,"# Age");
      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
    jk=1;        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    fprintf(ficresvij,"\n");
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  
    for(i=1,jk=1; i <=nlstate; i++){    xp=vector(1,npar);
      for(k=1; k <=(nlstate+ndeath); k++){    dnewm=matrix(1,nlstate,1,npar);
        if (k != i)    doldm=matrix(1,nlstate,1,nlstate);
          {    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
            printf("%d%d ",i,k);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
            fprintf(ficres,"%1d%1d ",i,k);  
            for(j=1; j <=ncovmodel; j++){    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
              printf("%f ",p[jk]);    gpp=vector(nlstate+1,nlstate+ndeath);
              fprintf(ficres,"%f ",p[jk]);    gmp=vector(nlstate+1,nlstate+ndeath);
              jk++;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
            }    
            printf("\n");    if(estepm < stepm){
            fprintf(ficres,"\n");      printf ("Problem %d lower than %d\n",estepm, stepm);
          }    }
      }    else  hstepm=estepm;   
    }    /* For example we decided to compute the life expectancy with the smallest unit */
  if(mle==1){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     /* Computing hessian and covariance matrix */       nhstepm is the number of hstepm from age to agelim 
     ftolhess=ftol; /* Usually correct */       nstepm is the number of stepm from age to agelin. 
     hesscov(matcov, p, npar, delti, ftolhess, func);       Look at function hpijx to understand why (it is linked to memory size questions) */
  }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");       survival function given by stepm (the optimization length). Unfortunately it
     printf("# Scales (for hessian or gradient estimation)\n");       means that if the survival funtion is printed every two years of age and if
      for(i=1,jk=1; i <=nlstate; i++){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       for(j=1; j <=nlstate+ndeath; j++){       results. So we changed our mind and took the option of the best precision.
         if (j!=i) {    */
           fprintf(ficres,"%1d%1d",i,j);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           printf("%1d%1d",i,j);    agelim = AGESUP;
           for(k=1; k<=ncovmodel;k++){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
             printf(" %.5e",delti[jk]);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             fprintf(ficres," %.5e",delti[jk]);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
             jk++;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
           printf("\n");      gp=matrix(0,nhstepm,1,nlstate);
           fprintf(ficres,"\n");      gm=matrix(0,nhstepm,1,nlstate);
         }  
       }  
      }      for(theta=1; theta <=npar; theta++){
            for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     k=1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     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");        }
     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");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     for(i=1;i<=npar;i++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       /*  if (k>nlstate) k=1;  
       i1=(i-1)/(ncovmodel*nlstate)+1;        if (popbased==1) {
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          if(mobilav ==0){
       printf("%s%d%d",alph[k],i1,tab[i]);*/            for(i=1; i<=nlstate;i++)
       fprintf(ficres,"%3d",i);              prlim[i][i]=probs[(int)age][i][ij];
       printf("%3d",i);          }else{ /* mobilav */ 
       for(j=1; j<=i;j++){            for(i=1; i<=nlstate;i++)
         fprintf(ficres," %.5e",matcov[i][j]);              prlim[i][i]=mobaverage[(int)age][i][ij];
         printf(" %.5e",matcov[i][j]);          }
       }        }
       fprintf(ficres,"\n");    
       printf("\n");        for(j=1; j<= nlstate; j++){
       k++;          for(h=0; h<=nhstepm; h++){
     }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                  gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     while((c=getc(ficpar))=='#' && c!= EOF){          }
       ungetc(c,ficpar);        }
       fgets(line, MAXLINE, ficpar);        /* This for computing probability of death (h=1 means
       puts(line);           computed over hstepm matrices product = hstepm*stepm months) 
       fputs(line,ficparo);           as a weighted average of prlim.
     }        */
     ungetc(c,ficpar);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     estepm=0;          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     if (estepm==0 || estepm < stepm) estepm=stepm;        }    
     if (fage <= 2) {        /* end probability of death */
       bage = ageminpar;  
       fage = agemaxpar;        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
            hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     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);        if (popbased==1) {
            if(mobilav ==0){
     while((c=getc(ficpar))=='#' && c!= EOF){            for(i=1; i<=nlstate;i++)
     ungetc(c,ficpar);              prlim[i][i]=probs[(int)age][i][ij];
     fgets(line, MAXLINE, ficpar);          }else{ /* mobilav */ 
     puts(line);            for(i=1; i<=nlstate;i++)
     fputs(line,ficparo);              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
   ungetc(c,ficpar);        }
    
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          for(h=0; h<=nhstepm; h++){
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                    gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);        /* This for computing probability of death (h=1 means
     puts(line);           computed over hstepm matrices product = hstepm*stepm months) 
     fputs(line,ficparo);           as a weighted average of prlim.
   }        */
   ungetc(c,ficpar);        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];
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        }    
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        /* end probability of death */
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);        for(j=1; j<= nlstate; j++) /* vareij */
   fprintf(ficparo,"pop_based=%d\n",popbased);            for(h=0; h<=nhstepm; h++){
   fprintf(ficres,"pop_based=%d\n",popbased);              gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     fgets(line, MAXLINE, ficpar);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     puts(line);        }
     fputs(line,ficparo);  
   }      } /* End theta */
   ungetc(c,ficpar);  
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);  
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);      for(h=0; h<=nhstepm; h++) /* veij */
 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=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     fgets(line, MAXLINE, ficpar);        for(theta=1; theta <=npar; theta++)
     puts(line);          trgradgp[j][theta]=gradgp[theta][j];
     fputs(line,ficparo);    
   }  
   ungetc(c,ficpar);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
   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=1;j<=nlstate;j++)
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          vareij[i][j][(int)age] =0.;
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  
       for(h=0;h<=nhstepm;h++){
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
 /*------------ gnuplot -------------*/          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);          for(i=1;i<=nlstate;i++)
              for(j=1;j<=nlstate;j++)
 /*------------ free_vector  -------------*/              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
  chdir(path);        }
        }
  free_ivector(wav,1,imx);    
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      /* pptj */
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
  free_ivector(num,1,n);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
  free_vector(agedc,1,n);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
  /*free_matrix(covar,1,NCOVMAX,1,n);*/        for(i=nlstate+1;i<=nlstate+ndeath;i++)
  fclose(ficparo);          varppt[j][i]=doldmp[j][i];
  fclose(ficres);      /* end ppptj */
       /*  x centered again */
 /*--------- index.htm --------*/      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
  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);   
       if (popbased==1) {
          if(mobilav ==0){
   /*--------------- Prevalence limit --------------*/          for(i=1; i<=nlstate;i++)
              prlim[i][i]=probs[(int)age][i][ij];
   strcpy(filerespl,"pl");        }else{ /* mobilav */ 
   strcat(filerespl,fileres);          for(i=1; i<=nlstate;i++)
   if((ficrespl=fopen(filerespl,"w"))==NULL) {            prlim[i][i]=mobaverage[(int)age][i][ij];
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        }
   }      }
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);               
   fprintf(ficrespl,"#Prevalence limit\n");      /* This for computing probability of death (h=1 means
   fprintf(ficrespl,"#Age ");         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);         as a weighted average of prlim.
   fprintf(ficrespl,"\n");      */
        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   prlim=matrix(1,nlstate,1,nlstate);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      }    
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      /* end probability of death */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   k=0;      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   agebase=ageminpar;        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   agelim=agemaxpar;        for(i=1; i<=nlstate;i++){
   ftolpl=1.e-10;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   i1=cptcoveff;        }
   if (cptcovn < 1){i1=1;}      } 
       fprintf(ficresprobmorprev,"\n");
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      fprintf(ficresvij,"%.0f ",age );
         k=k+1;      for(i=1; i<=nlstate;i++)
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        for(j=1; j<=nlstate;j++){
         fprintf(ficrespl,"\n#******");          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         for(j=1;j<=cptcoveff;j++)        }
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficresvij,"\n");
         fprintf(ficrespl,"******\n");      free_matrix(gp,0,nhstepm,1,nlstate);
              free_matrix(gm,0,nhstepm,1,nlstate);
         for (age=agebase; age<=agelim; age++){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
           fprintf(ficrespl,"%.0f",age );      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           for(i=1; i<=nlstate;i++)    } /* End age */
           fprintf(ficrespl," %.5f", prlim[i][i]);    free_vector(gpp,nlstate+1,nlstate+ndeath);
           fprintf(ficrespl,"\n");    free_vector(gmp,nlstate+1,nlstate+ndeath);
         }    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
       }    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     }    fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
   fclose(ficrespl);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*------------- h Pij x at various ages ------------*/  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
   }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
   printf("Computing pij: result on file '%s' \n", filerespij);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
      fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    /*  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);
   /*if (stepm<=24) stepsize=2;*/  */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   agelim=AGESUP;    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    free_vector(xp,1,npar);
      free_matrix(doldm,1,nlstate,1,nlstate);
   k=0;    free_matrix(dnewm,1,nlstate,1,npar);
   for(cptcov=1;cptcov<=i1;cptcov++){    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
       k=k+1;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         fprintf(ficrespij,"\n#****** ");    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         for(j=1;j<=cptcoveff;j++)    fclose(ficresprobmorprev);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fflush(ficgp);
         fprintf(ficrespij,"******\n");    fflush(fichtm); 
          }  /* end varevsij */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  /************ Variance of prevlim ******************/
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  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[])
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  {
           oldm=oldms;savm=savms;    /* Variance of prevalence limit */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
           fprintf(ficrespij,"# Age");    double **newm;
           for(i=1; i<=nlstate;i++)    double **dnewm,**doldm;
             for(j=1; j<=nlstate+ndeath;j++)    int i, j, nhstepm, hstepm;
               fprintf(ficrespij," %1d-%1d",i,j);    int k, cptcode;
           fprintf(ficrespij,"\n");    double *xp;
            for (h=0; h<=nhstepm; h++){    double *gp, *gm;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    double **gradg, **trgradg;
             for(i=1; i<=nlstate;i++)    double age,agelim;
               for(j=1; j<=nlstate+ndeath;j++)    int theta;
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    
             fprintf(ficrespij,"\n");    pstamp(ficresvpl);
              }    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficresvpl,"# Age");
           fprintf(ficrespij,"\n");    for(i=1; i<=nlstate;i++)
         }        fprintf(ficresvpl," %1d-%1d",i,i);
     }    fprintf(ficresvpl,"\n");
   }  
     xp=vector(1,npar);
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
   fclose(ficrespij);    
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
   /*---------- Forecasting ------------------*/    agelim = AGESUP;
   if((stepm == 1) && (strcmp(model,".")==0)){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);      if (stepm >= YEARM) hstepm=1;
   }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   else{      gradg=matrix(1,npar,1,nlstate);
     erreur=108;      gp=vector(1,nlstate);
     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);      gm=vector(1,nlstate);
   }  
        for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
   /*---------- Health expectancies and variances ------------*/          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
   strcpy(filerest,"t");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   strcat(filerest,fileres);        for(i=1;i<=nlstate;i++)
   if((ficrest=fopen(filerest,"w"))==NULL) {          gp[i] = prlim[i][i];
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      
   }        for(i=1; i<=npar; i++) /* Computes gradient */
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
   strcpy(filerese,"e");          gm[i] = prlim[i][i];
   strcat(filerese,fileres);  
   if((ficreseij=fopen(filerese,"w"))==NULL) {        for(i=1;i<=nlstate;i++)
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   }      } /* End theta */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
       trgradg =matrix(1,nlstate,1,npar);
  strcpy(fileresv,"v");  
   strcat(fileresv,fileres);      for(j=1; j<=nlstate;j++)
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        for(theta=1; theta <=npar; theta++)
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          trgradg[j][theta]=gradg[theta][j];
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      for(i=1;i<=nlstate;i++)
   calagedate=-1;        varpl[i][(int)age] =0.;
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   k=0;      for(i=1;i<=nlstate;i++)
   for(cptcov=1;cptcov<=i1;cptcov++){        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;      fprintf(ficresvpl,"%.0f ",age );
       fprintf(ficrest,"\n#****** ");      for(i=1; i<=nlstate;i++)
       for(j=1;j<=cptcoveff;j++)        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficresvpl,"\n");
       fprintf(ficrest,"******\n");      free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       fprintf(ficreseij,"\n#****** ");      free_matrix(gradg,1,npar,1,nlstate);
       for(j=1;j<=cptcoveff;j++)      free_matrix(trgradg,1,nlstate,1,npar);
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    } /* End age */
       fprintf(ficreseij,"******\n");  
     free_vector(xp,1,npar);
       fprintf(ficresvij,"\n#****** ");    free_matrix(doldm,1,nlstate,1,npar);
       for(j=1;j<=cptcoveff;j++)    free_matrix(dnewm,1,nlstate,1,nlstate);
         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);  /************ Variance of one-step probabilities  ******************/
       oldm=oldms;savm=savms;  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[])
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);    {
      int i, j=0,  i1, k1, l1, t, tj;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    int k2, l2, j1,  z1;
       oldm=oldms;savm=savms;    int k=0,l, cptcode;
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);    int first=1, first1, first2;
        double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
      double *xp;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    double *gp, *gm;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    double **gradg, **trgradg;
       fprintf(ficrest,"\n");    double **mu;
     double age,agelim, cov[NCOVMAX+1];
       epj=vector(1,nlstate+1);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
       for(age=bage; age <=fage ;age++){    int theta;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    char fileresprob[FILENAMELENGTH];
         if (popbased==1) {    char fileresprobcov[FILENAMELENGTH];
           for(i=1; i<=nlstate;i++)    char fileresprobcor[FILENAMELENGTH];
             prlim[i][i]=probs[(int)age][i][k];    double ***varpij;
         }  
            strcpy(fileresprob,"prob"); 
         fprintf(ficrest," %4.0f",age);    strcat(fileresprob,fileres);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      printf("Problem with resultfile: %s\n", fileresprob);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    }
           }    strcpy(fileresprobcov,"probcov"); 
           epj[nlstate+1] +=epj[j];    strcat(fileresprobcov,fileres);
         }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
         for(i=1, vepp=0.;i <=nlstate;i++)      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
           for(j=1;j <=nlstate;j++)    }
             vepp += vareij[i][j][(int)age];    strcpy(fileresprobcor,"probcor"); 
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    strcat(fileresprobcor,fileres);
         for(j=1;j <=nlstate;j++){    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));      printf("Problem with resultfile: %s\n", fileresprobcor);
         }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
         fprintf(ficrest,"\n");    }
       }    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     }    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   }    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
 free_matrix(mint,1,maxwav,1,n);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     free_vector(weight,1,n);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   fclose(ficreseij);    pstamp(ficresprob);
   fclose(ficresvij);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   fclose(ficrest);    fprintf(ficresprob,"# Age");
   fclose(ficpar);    pstamp(ficresprobcov);
   free_vector(epj,1,nlstate+1);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
      fprintf(ficresprobcov,"# Age");
   /*------- Variance limit prevalence------*/      pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   strcpy(fileresvpl,"vpl");    fprintf(ficresprobcor,"# Age");
   strcat(fileresvpl,fileres);  
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    for(i=1; i<=nlstate;i++)
     exit(0);      for(j=1; j<=(nlstate+ndeath);j++){
   }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
   k=0;      }  
   for(cptcov=1;cptcov<=i1;cptcov++){   /* fprintf(ficresprob,"\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficresprobcov,"\n");
       k=k+1;    fprintf(ficresprobcor,"\n");
       fprintf(ficresvpl,"\n#****** ");   */
       for(j=1;j<=cptcoveff;j++)    xp=vector(1,npar);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       fprintf(ficresvpl,"******\n");    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
          mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
       oldm=oldms;savm=savms;    first=1;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    fprintf(ficgp,"\n# Routine varprob");
     }    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
  }    fprintf(fichtm,"\n");
   
   fclose(ficresvpl);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
   /*---------- End : free ----------------*/    file %s<br>\n",optionfilehtmcov);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
    and drawn. It helps understanding how is the covariance between two incidences.\
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    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 \
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  standard deviations wide on each axis. <br>\
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
    
   free_matrix(matcov,1,npar,1,npar);    cov[1]=1;
   free_vector(delti,1,npar);    /* tj=cptcoveff; */
   free_matrix(agev,1,maxwav,1,imx);    tj = (int) pow(2,cptcoveff);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
   if(erreur >0)    for(j1=1; j1<=tj;j1++){
     printf("End of Imach with error or warning %d\n",erreur);      /*for(i1=1; i1<=ncodemax[t];i1++){ */
   else   printf("End of Imach\n");      /*j1++;*/
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */        if  (cptcovn>0) {
            fprintf(ficresprob, "\n#********** Variable "); 
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /*printf("Total time was %d uSec.\n", total_usecs);*/          fprintf(ficresprob, "**********\n#\n");
   /*------ End -----------*/          fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
  end:          
 #ifdef windows          fprintf(ficgp, "\n#********** Variable "); 
   /* chdir(pathcd);*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 #endif          fprintf(ficgp, "**********\n#\n");
  /*system("wgnuplot graph.plt");*/          
  /*system("../gp37mgw/wgnuplot graph.plt");*/          
  /*system("cd ../gp37mgw");*/          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
  strcpy(plotcmd,GNUPLOTPROGRAM);          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
  strcat(plotcmd," ");          
  strcat(plotcmd,optionfilegnuplot);          fprintf(ficresprobcor, "\n#********** Variable ");    
  system(plotcmd);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
 #ifdef windows        }
   while (z[0] != 'q') {        
     /* chdir(path); */        gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");        trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     scanf("%s",z);        gp=vector(1,(nlstate)*(nlstate+ndeath));
     if (z[0] == 'c') system("./imach");        gm=vector(1,(nlstate)*(nlstate+ndeath));
     else if (z[0] == 'e') system(optionfilehtm);        for (age=bage; age<=fage; age ++){ 
     else if (z[0] == 'g') system(plotcmd);          cov[2]=age;
     else if (z[0] == 'q') exit(0);          for (k=1; k<=cptcovn;k++) {
   }            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
 #endif                                                           * 1  1 1 1 1
 }                                                           * 2  2 1 1 1
                                                            * 3  1 2 1 1
                                                            */
             /* nbcode[1][1]=0 nbcode[1][2]=1;*/
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
         free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nunset parametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;first2=2;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     if ((lc2 <0) || (lc1 <0) ){
                       if(first2==1){
                         first1=0;
                       printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
                       }
                       fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
                       /* lc1=fabs(lc1); */ /* If we want to have them positive */
                       /* lc2=fabs(lc2); */
                     }
   
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small size 320, 240");
                       fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
         /* } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      fprintf(fichtm,"\
    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Population projections by age and states: \
      <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
   <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
   <img src=\"%s%d_%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
    fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
   <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
   true period expectancies (those weighted with period prevalences are also\
    drawn in addition to the population based expectancies computed using\
    observed and cahotic prevalences: %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
     int ng=0;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
        fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else        fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l lt 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
         else fprintf(ficgp,"\" t\"\" w l lt 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small size 320, 240\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small size 320, 240\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
     /*goto avoid;*/
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;/* To be checked else nbcode[0][0] wrong */
                for(j=3; j <=ncovmodel; j++) {
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
                  /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
                  /*        ij++; */
                  /* } */
                  /* else */
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
                    /*   fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
                    /*   ij++; */
                    /* } */
                    /* else */
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
    avoid:
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   #ifdef GSL
   /******************* Gompertz_f Likelihood ******************************/
   double gompertz_f(const gsl_vector *v, void *params)
   { 
     double A,B,LL=0.0,sump=0.,num=0.;
     double *x= (double *) v->data;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
     printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
                +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           LL=LL+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
     printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
    
     return -2*LL*num/sump;
   }
   #endif
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small size 320, 240\n set log y\n"); 
     /* fprintf(ficgp, "set size 0.65,0.65\n"); */
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   int readdata(char datafile[], int firstobs, int lastobs, int *imax)
   {
   
     /*-------- data file ----------*/
     FILE *fic;
     char dummy[]="                         ";
     int i, j, n;
     int linei, month, year,iout;
     char line[MAXLINE], linetmp[MAXLINE];
     char stra[80], strb[80];
     char *stratrunc;
     int lstra;
   
   
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);return 1;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
     }
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
       trimbb(linetmp,line); /* Trims multiple blanks in line */
       for (j=0; line[j]!='\0';j++){
         line[j]=linetmp[j];
       }
     
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb, line, ' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.",dummy) != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
           return 1;
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.", dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
       }
       if (year==9999) {
         printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given.  Exiting.\n",strb, linei,i,line);
         fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
           return 1;
   
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         fflush(ficlog);
         return 1;
       }
       weight[i]=dval; 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         if(strb[0]=='.') { /* Missing status */
           lval=-1;
         }else{
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);
             fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative).  Exiting.\n",lval, linei,i, line);fflush(ficlog);
             return 1;
           }
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);
           fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
           return 1;
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       }  
       lstra=strlen(stra);
        
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
   
     *imax=i-1; /* Number of individuals */
     fclose(fic);
    
     return (0);
     endread:
       printf("Exiting readdata: ");
       fclose(fic);
       return (1);
   
   
   
   }
   void removespace(char *str) {
     char *p1 = str, *p2 = str;
     do
       while (*p2 == ' ')
         p2++;
     while (*p1++ = *p2++);
   }
   
   int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
      * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
      * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
      * - cptcovn or number of covariates k of the models excluding age*products =6
      * - cptcovage number of covariates with age*products =2
      * - cptcovs number of simple covariates
      * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
      *     which is a new column after the 9 (ncovcol) variables. 
      * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
      * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
      *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
      * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
    */
   {
     int i, j, k, ks;
     int i1, j1, k1, k2;
     char modelsav[80];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     /*removespace(model);*/
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
       j=nbocc(model,'+'); /**< j=Number of '+' */
       j1=nbocc(model,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
       cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                     /* including age products which are counted in cptcovage.
                     /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
       strcpy(modelsav,model); 
       if (strstr(model,"AGE") !=0){
         printf("Error. AGE must be in lower case 'age' model=%s ",model);
         fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
         return 1;
       }
       if (strstr(model,"v") !=0){
         printf("Error. 'v' must be in upper case 'V' model=%s ",model);
         fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
         return 1;
       }
       
       /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
        *  <          ncovcol=8                >
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
        *  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        *How to reorganize?
        * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
        * Tvars {2,   1,     3,      3,   11,     10,     8,       8,   7,   8,   5,  6}
        *       {2,   1,     4,      8,    5,      6,     3,       7}
        * Struct []
        */
   
       /* This loop fills the array Tvar from the string 'model'.*/
       /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
       /*   modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4  */
       /*  k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
       /*  k=3 V4 Tvar[k=3]= 4 (from V4) */
       /*  k=2 V1 Tvar[k=2]= 1 (from V1) */
       /*  k=1 Tvar[1]=2 (from V2) */
       /*  k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */
       /*  cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
       /*  } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
       /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates */
           Tvar[k]=0;
       cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
                                        modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
           cutl(strc,strd,strb,'*'); /**< strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
             /* covar is not filled and then is empty */
             cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
             cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tage[1] = 4 */
             /*printf("stre=%s ", stre);*/
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutl(stre,strb,strc,'V');
             Tvar[k]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=k;
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
             cptcovn++;
             cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
                                     because this model-covariate is a construction we invent a new column
                                     ncovcol + k1
                                     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                     Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;
             Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
             Tvar[cptcovt+k2+1]=Tvard[k1][2];  /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
             for (i=1; i<=lastobs;i++){
               /* Computes the new covariate which is a product of
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }
           } /* End age is not in the model */
         } /* End if model includes a product */
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates */
           cptcovn++;
           Tvar[k]=atoi(strd);
         }
         strcpy(modelsav,stra);  /* modelsav=V2+V1+V4 stra=V2+V1+V4 */ 
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
   
     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
     endread:
       printf("Exiting decodemodel: ");
       return (1);
   }
   
   calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
   {
     int i, m;
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           *nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] < *agemin){ 
               *agemin=agev[m][i];
               printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
             }
             else if(agev[m][i] >*agemax){
               *agemax=agev[m][i];
               printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           *nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           return 1;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
     return (0);
     endread:
       printf("Exiting calandcheckages: ");
       return (1);
   }
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
   #ifdef GSL
     const gsl_multimin_fminimizer_type *T;
     size_t iteri = 0, it;
     int rval = GSL_CONTINUE;
     int status = GSL_SUCCESS;
     double ssval;
   #endif
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
     int vpopbased=0;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
     int *dcwave;
   
     char z[1]="c", occ;
   
     /*char  *strt;*/
     char strtend[80];
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Dirty */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line,stdout);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       fputs(line, stdout);
       //puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
     /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
        v1+v2*age+v2*v3 makes cptcovn = 3
     */
     if (strlen(model)>1) 
       ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
     else
       ncovmodel=2;
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
     npar= nforce*ncovmodel; /* Number of parameters like aij*/
     if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
       printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
       fflush(stdout);
       fclose (ficlog);
       goto end;
     }
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       goto end;
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guessed parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       /* Reads scales values */
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       /* Reads covariance matrix */
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++)
         for(j=1; j <=npar; j++) matcov[i][j]=0.;
         
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   
     n= lastobs;
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   
     /* Reads data from file datafile */
     if (readdata(datafile, firstobs, lastobs, &imx)==1)
       goto end;
   
     /* Calculation of the number of parameters from char model */
       /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
           k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
           k=3 V4 Tvar[k=3]= 4 (from V4)
           k=2 V1 Tvar[k=2]= 1 (from V1)
           k=1 Tvar[1]=2 (from V2)
       */
     Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
         Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
     */
     /* For model-covariate k tells which data-covariate to use but
       because this model-covariate is a construction we invent a new column
       ncovcol + k1
       If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
       Tvar[3=V1*V4]=4+1 etc */
     Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
     /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
        if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)
     */
     Tvaraff=ivector(1,NCOVMAX); /* Unclear */
     Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                               * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                            4 covariates (3 plus signs)
                            Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                         */  
   
     if(decodemodel(model, lastobs) == 1)
       goto end;
   
     if((double)(lastobs-imx)/(double)imx > 1.10){
       nbwarn++;
       printf("Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
       fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n  effective number of cases imx=%d, please adjust, \n  otherwise you are allocating more memory than necessary.\n",lastobs, imx); 
     }
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
       for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
     }
   
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
       goto end;
   
   
     agegomp=(int)agemin;
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
     /* */
     
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
     /* */
    
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     Ndum =ivector(-1,NCOVMAX);  
     if (ncovmodel > 2)
       tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
   
     codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
     /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
     h=0;
   
   
     /*if (cptcovn > 0) */
         
    
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
       for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */ 
         for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
           for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */ 
             h++;
             if (h>m) 
               h=1;
             /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
              *     h     1     2     3     4
              *______________________________  
              *     1 i=1 1 i=1 1 i=1 1 i=1 1
              *     2     2     1     1     1
              *     3 i=2 1     2     1     1
              *     4     2     2     1     1
              *     5 i=3 1 i=2 1     2     1
              *     6     2     1     2     1
              *     7 i=4 1     2     2     1
              *     8     2     2     2     1
              *     9 i=5 1 i=3 1 i=2 1     1
              *    10     2     1     1     1
              *    11 i=6 1     2     1     1
              *    12     2     2     1     1
              *    13 i=7 1 i=4 1     2     1    
              *    14     2     1     2     1
              *    15 i=8 1     2     2     1
              *    16     2     2     2     1
              */
             codtab[h][k]=j;
             /*codtab[h][Tvar[k]]=j;*/
             printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
          printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
   
    free_ivector(Ndum,-1,NCOVMAX);
   
   
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       //fprintf(ficgp,"set missing 'NaNq'\n");
       fprintf(ficgp,"set datafile missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);
       exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM); 
   /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       /*p[1]=0.0268; p[NDIM]=0.083;*/
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
   #ifdef GSL
       printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
   #elsedef
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
   #endif
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
   #ifdef GSL
       fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
   #elsedef
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
   #endif
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
   #ifdef GSL
       /* gsl starts here */ 
       T = gsl_multimin_fminimizer_nmsimplex;
       gsl_multimin_fminimizer *sfm = NULL;
       gsl_vector *ss, *x;
       gsl_multimin_function minex_func;
   
       /* Initial vertex size vector */
       ss = gsl_vector_alloc (NDIM);
       
       if (ss == NULL){
         GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
       }
       /* Set all step sizes to 1 */
       gsl_vector_set_all (ss, 0.001);
   
       /* Starting point */
       
       x = gsl_vector_alloc (NDIM);
       
       if (x == NULL){
         gsl_vector_free(ss);
         GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
       }
     
       /* Initialize method and iterate */
       /*     p[1]=0.0268; p[NDIM]=0.083; */
   /*     gsl_vector_set(x, 0, 0.0268); */
   /*     gsl_vector_set(x, 1, 0.083); */
       gsl_vector_set(x, 0, p[1]);
       gsl_vector_set(x, 1, p[2]);
   
       minex_func.f = &gompertz_f;
       minex_func.n = NDIM;
       minex_func.params = (void *)&p; /* ??? */
       
       sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
       gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
       
       printf("Iterations beginning .....\n\n");
       printf("Iter. #    Intercept       Slope     -Log Likelihood     Simplex size\n");
   
       iteri=0;
       while (rval == GSL_CONTINUE){
         iteri++;
         status = gsl_multimin_fminimizer_iterate(sfm);
         
         if (status) printf("error: %s\n", gsl_strerror (status));
         fflush(0);
         
         if (status) 
           break;
         
         rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
         ssval = gsl_multimin_fminimizer_size (sfm);
         
         if (rval == GSL_SUCCESS)
           printf ("converged to a local maximum at\n");
         
         printf("%5d ", iteri);
         for (it = 0; it < NDIM; it++){
           printf ("%10.5f ", gsl_vector_get (sfm->x, it));
         }
         printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
       }
       
       printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
       
       gsl_vector_free(x); /* initial values */
       gsl_vector_free(ss); /* inital step size */
       for (it=0; it<NDIM; it++){
         p[it+1]=gsl_vector_get(sfm->x,it);
         fprintf(ficrespow," %.12lf", p[it]);
       }
       gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
   #endif
   #ifdef POWELL
        powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
   #endif  
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
   #ifdef GSL
       free_ivector(cens,1,n);
       free_vector(agecens,1,n);
       free_ivector(dcwave,1,n);
       free_matrix(ximort,1,NDIM,1,NDIM);
   #endif
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
       globpr=0;/* debug */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         fputs(line,stdout);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
        /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
       /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
       
       replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
   #include "prevlim.h"  /* Use ficrespl, ficlog */
       fclose(ficrespl);
   
   #ifdef FREEEXIT2
   #include "freeexit2.h"
   #endif
   
       /*------------- h Pij x at various ages ------------*/
   #include "hpijx.h"
       fclose(ficrespij);
   
     /*-------------- Variance of one-step probabilities---*/
       k=1;
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
   
       /*---------- Health expectancies, no variances ------------*/
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficreseij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
         
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       fclose(ficreseij);
   
   
       /*---------- Health expectancies and variances ------------*/
   
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
           /*
            */
           /* goto endfree; */
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           pstamp(ficrest);
   
   
           for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
             oldm=oldms;savm=savms; /* Segmentation fault */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
             fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
             if(vpopbased==1)
               fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
             else
               fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
             fprintf(ficrest,"# Age e.. (std) ");
             for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
             fprintf(ficrest,"\n");
   
             epj=vector(1,nlstate+1);
             for(age=bage; age <=fage ;age++){
               prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
               if (vpopbased==1) {
                 if(mobilav ==0){
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=probs[(int)age][i][k];
                 }else{ /* mobilav */ 
                   for(i=1; i<=nlstate;i++)
                     prlim[i][i]=mobaverage[(int)age][i][k];
                 }
               }
           
               fprintf(ficrest," %4.0f",age);
               for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                 for(i=1, epj[j]=0.;i <=nlstate;i++) {
                   epj[j] += prlim[i][i]*eij[i][j][(int)age];
                   /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                 }
                 epj[nlstate+1] +=epj[j];
               }
   
               for(i=1, vepp=0.;i <=nlstate;i++)
                 for(j=1;j <=nlstate;j++)
                   vepp += vareij[i][j][(int)age];
               fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
               for(j=1;j <=nlstate;j++){
                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
               }
               fprintf(ficrest,"\n");
             }
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         /*}*/
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
             
       for (k=1; k <= (int) pow(2,cptcoveff); k++){
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }  /* mle==-3 arrives here for freeing */
    endfree:
       free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,NCOVMAX);
       free_ivector(Tvar,1,NCOVMAX);
       free_ivector(Tprod,1,NCOVMAX);
       free_ivector(Tvaraff,1,NCOVMAX);
       free_ivector(Tage,1,NCOVMAX);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.46  
changed lines
  Added in v.1.147


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